Starting phenix.real_space_refine on Fri Oct 30 06:50:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xte_67203/10_2026/9xte_67203.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xte_67203/10_2026/9xte_67203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xte_67203/10_2026/9xte_67203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xte_67203/10_2026/9xte_67203.map" model { file = "/net/cci-nas-00/data/ceres_data/9xte_67203/10_2026/9xte_67203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xte_67203/10_2026/9xte_67203.cif" } resolution = 2.24 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= 0.002 sd= 0.063 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 1026 5.49 5 Mg 34 5.21 5 S 46 5.16 5 C 16839 2.51 5 N 6187 2.21 5 O 11380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s 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: 35512 Number of models: 1 Model: "" Number of chains: 23 Chain: "D" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1633 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 6, 'TRANS': 197} Chain: "E" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1143 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "F" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 824 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} 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: "L" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "O" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "P" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "T" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "A" Number of atoms: 22039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 22039 Classifications: {'RNA': 1025, 'RNAv2': 1} Modifications used: {'rna2p_pur': 81, 'rna2p_pyr': 52, 'rna3p': 2, 'rna3p_pur': 509, 'rna3p_pyr': 382} Link IDs: {'rna2p': 133, 'rna3p': 892} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 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: "K" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 858 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Unusual residues: {' MG': 34} Classifications: {'undetermined': 34} Link IDs: {None: 33} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "O" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "P" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "Q" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "T" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1996, 1996 Classifications: {'water': 1996} Link IDs: {None: 1995} Time building chain proxies: 7.03, per 1000 atoms: 0.20 Number of scatterers: 35512 At special positions: 0 Unit cell: (132.902, 174.326, 203.668, 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 1026 15.00 Mg 34 11.99 O 11380 8.00 N 6187 7.00 C 16839 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: 2.64 Conformation dependent library (CDL) restraints added in 866.6 milliseconds 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 13 sheets defined 44.2% alpha, 20.9% beta 354 base pairs and 563 stacking pairs defined. Time for finding SS restraints: 5.48 Creating SS restraints... Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.226A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 31 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.689A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 152 through 163 removed outlier: 3.694A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 205 Processing helix chain 'E' and resid 55 through 70 removed outlier: 3.657A pdb=" N ARG E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) 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 157 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 12 through 16 removed outlier: 5.006A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 32 removed outlier: 3.550A pdb=" N ARG F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 79 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: 3.660A pdb=" N LEU H 92 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 120 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 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 47 removed outlier: 3.920A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS O 47 " --> pdb=" O PHE O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.591A pdb=" N TYR O 78 " --> pdb=" O ASP O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 63 Processing helix chain 'P' and resid 68 through 81 Processing helix chain 'Q' and resid 49 through 52 removed outlier: 4.358A pdb=" N GLU Q 52 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 49 through 52' Processing helix chain 'R' and resid 25 through 32 removed outlier: 4.009A pdb=" N LEU R 29 " --> pdb=" O ASP R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'T' and resid 4 through 42 Processing helix chain 'T' and resid 44 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 86 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 73 through 87 removed outlier: 4.593A pdb=" N GLU B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ALA B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 123 removed outlier: 3.847A pdb=" N GLN B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 130 through 148 removed outlier: 3.912A pdb=" N GLU B 140 " --> pdb=" O MET B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 206 through 227 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: 3.560A 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: 3.654A pdb=" N ARG K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.880A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 12 through 24 removed outlier: 5.426A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.318A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 39 through 45 removed outlier: 6.451A pdb=" N LEU F 39 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN F 63 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASP F 41 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU F 61 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL F 60 " --> pdb=" O PHE F 8 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE F 8 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.976A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.523A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.523A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE H 125 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 29 through 40 removed outlier: 5.698A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N VAL L 93 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR L 64 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 50 through 52 removed outlier: 6.130A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 8 through 17 removed outlier: 7.782A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP Q 15 " --> pdb=" O SER Q 20 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER Q 20 " --> pdb=" O ASP Q 15 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N LYS Q 71 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N HIS Q 45 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL Q 78 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL Q 58 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 31 through 35 Processing sheet with id=AB3, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.129A pdb=" N LEU B 68 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B 161 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE B 186 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 163 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL B 183 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE B 200 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 185 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 42 through 45 removed outlier: 3.657A pdb=" N GLY K 42 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE K 30 " --> pdb=" O HIS K 23 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY K 18 " --> pdb=" O ASN K 80 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL K 83 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE K 109 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL K 85 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP K 111 " --> pdb=" O VAL K 85 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1629 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 890 hydrogen bonds 1428 hydrogen bond angles 0 basepair planarities 354 basepair parallelities 563 stacking parallelities Total time for adding SS restraints: 37.33 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4567 1.32 - 1.46: 16359 1.46 - 1.59: 13670 1.59 - 1.72: 1373 1.72 - 1.86: 81 Bond restraints: 36050 Sorted by residual: bond pdb=" C8 G A 111 " pdb=" N7 G A 111 " ideal model delta sigma weight residual 1.305 1.275 0.030 6.00e-03 2.78e+04 2.50e+01 bond pdb=" C8 G A 108 " pdb=" N7 G A 108 " ideal model delta sigma weight residual 1.305 1.277 0.028 6.00e-03 2.78e+04 2.12e+01 bond pdb=" C8 G A 388 " pdb=" N7 G A 388 " ideal model delta sigma weight residual 1.305 1.279 0.026 6.00e-03 2.78e+04 1.94e+01 bond pdb=" C8 G A 292 " pdb=" N7 G A 292 " ideal model delta sigma weight residual 1.305 1.280 0.025 6.00e-03 2.78e+04 1.79e+01 bond pdb=" N9 A A 119 " pdb=" C4 A A 119 " ideal model delta sigma weight residual 1.374 1.349 0.025 6.00e-03 2.78e+04 1.77e+01 ... (remaining 36045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 50062 1.98 - 3.96: 3569 3.96 - 5.94: 117 5.94 - 7.93: 15 7.93 - 9.91: 3 Bond angle restraints: 53766 Sorted by residual: angle pdb=" O5' G A 376 " pdb=" C5' G A 376 " pdb=" C4' G A 376 " ideal model delta sigma weight residual 109.40 114.68 -5.28 8.00e-01 1.56e+00 4.36e+01 angle pdb=" O5' U A 916 " pdb=" C5' U A 916 " pdb=" C4' U A 916 " ideal model delta sigma weight residual 109.40 113.93 -4.53 8.00e-01 1.56e+00 3.20e+01 angle pdb=" C2 C A 83 " pdb=" N3 C A 83 " pdb=" C4 C A 83 " ideal model delta sigma weight residual 119.90 117.14 2.76 5.00e-01 4.00e+00 3.04e+01 angle pdb=" O5' C A 436 " pdb=" C5' C A 436 " pdb=" C4' C A 436 " ideal model delta sigma weight residual 109.40 113.69 -4.29 8.00e-01 1.56e+00 2.87e+01 angle pdb=" O4' A A 496 " pdb=" C1' A A 496 " pdb=" N9 A A 496 " ideal model delta sigma weight residual 108.50 112.21 -3.71 7.00e-01 2.04e+00 2.80e+01 ... (remaining 53761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 20289 35.45 - 70.91: 2518 70.91 - 106.36: 275 106.36 - 141.82: 7 141.82 - 177.27: 3 Dihedral angle restraints: 23092 sinusoidal: 18989 harmonic: 4103 Sorted by residual: 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 65.60 134.40 1 1.50e+01 4.44e-03 7.25e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 66.36 133.64 1 1.50e+01 4.44e-03 7.21e+01 dihedral pdb=" O4' C A 183 " pdb=" C1' C A 183 " pdb=" N1 C A 183 " pdb=" C2 C A 183 " ideal model delta sinusoidal sigma weight residual -128.00 49.27 -177.27 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 23089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 5730 0.098 - 0.196: 1097 0.196 - 0.293: 13 0.293 - 0.391: 0 0.391 - 0.489: 2 Chirality restraints: 6842 Sorted by residual: chirality pdb=" P C A 528 " pdb=" OP1 C A 528 " pdb=" OP2 C A 528 " pdb=" O5' C A 528 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" P C A 526 " pdb=" OP1 C A 526 " pdb=" OP2 C A 526 " pdb=" O5' C A 526 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" C1' C A 519 " pdb=" O4' C A 519 " pdb=" C2' C A 519 " pdb=" N1 C A 519 " both_signs ideal model delta sigma weight residual False 2.47 2.19 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 6839 not shown) Planarity restraints: 3002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 362 " -0.054 2.00e-02 2.50e+03 2.26e-02 1.54e+01 pdb=" N9 G A 362 " 0.050 2.00e-02 2.50e+03 pdb=" C8 G A 362 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G A 362 " 0.010 2.00e-02 2.50e+03 pdb=" C5 G A 362 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A 362 " -0.015 2.00e-02 2.50e+03 pdb=" O6 G A 362 " -0.013 2.00e-02 2.50e+03 pdb=" N1 G A 362 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G A 362 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G A 362 " 0.010 2.00e-02 2.50e+03 pdb=" N3 G A 362 " 0.010 2.00e-02 2.50e+03 pdb=" C4 G A 362 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 324 " 0.047 2.00e-02 2.50e+03 2.11e-02 1.33e+01 pdb=" N9 G A 324 " -0.048 2.00e-02 2.50e+03 pdb=" C8 G A 324 " -0.017 2.00e-02 2.50e+03 pdb=" N7 G A 324 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A 324 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G A 324 " 0.013 2.00e-02 2.50e+03 pdb=" O6 G A 324 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G A 324 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 324 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G A 324 " -0.014 2.00e-02 2.50e+03 pdb=" N3 G A 324 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 324 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 387 " -0.045 2.00e-02 2.50e+03 2.22e-02 1.11e+01 pdb=" N1 U A 387 " 0.041 2.00e-02 2.50e+03 pdb=" C2 U A 387 " 0.006 2.00e-02 2.50e+03 pdb=" O2 U A 387 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U A 387 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U A 387 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U A 387 " -0.017 2.00e-02 2.50e+03 pdb=" C5 U A 387 " -0.006 2.00e-02 2.50e+03 pdb=" C6 U A 387 " 0.018 2.00e-02 2.50e+03 ... (remaining 2999 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 330 2.41 - 3.03: 20929 3.03 - 3.65: 71816 3.65 - 4.28: 113245 4.28 - 4.90: 146211 Nonbonded interactions: 352531 Sorted by model distance: nonbonded pdb=" OP2 G A 100 " pdb="MG MG A1634 " model vdw 1.782 2.170 nonbonded pdb=" OP2 C A 352 " pdb="MG MG A1629 " model vdw 1.811 2.170 nonbonded pdb=" OP2 A A 608 " pdb="MG MG A1621 " model vdw 1.823 2.170 nonbonded pdb=" OP2 A A 573 " pdb="MG MG A1633 " model vdw 1.861 2.170 nonbonded pdb=" OP2 A A 441 " pdb="MG MG A1623 " model vdw 1.873 2.170 ... (remaining 352526 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: 8.090 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: 0.040 Extract box with map and model: 0.780 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 64.410 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 : 0.007 0.053 36050 Z= 0.759 Angle : 0.934 9.907 53766 Z= 0.784 Chirality : 0.064 0.489 6842 Planarity : 0.006 0.055 3002 Dihedral : 22.823 177.274 20444 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % 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: 0.17 (0.22), residues: 1406 helix: 1.00 (0.21), residues: 561 sheet: -0.06 (0.32), residues: 247 loop : -0.58 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 25 TYR 0.029 0.002 TYR L 117 PHE 0.015 0.002 PHE Q 37 TRP 0.019 0.002 TRP P 60 HIS 0.009 0.001 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.76 (36050) covalent geometry : angle 0.93433 / 0.78 (53766) hydrogen bonds : bond 0.11139 / 7.45 ( 1457) hydrogen bonds : angle 4.66947 / 3.31 ( 3057) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.763 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: symmetry clash revert: symmetry clash REVERT: O 35 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7662 (mt0) REVERT: O 48 LYS cc_start: 0.8207 (mmtp) cc_final: 0.7744 (mtmt) REVERT: P 66 THR cc_start: 0.8931 (m) cc_final: 0.8727 (p) REVERT: P 76 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8078 (mttp) REVERT: Q 57 ASP cc_start: 0.7587 (m-30) cc_final: 0.7190 (m-30) REVERT: B 27 MET cc_start: 0.7115 (mmm) cc_final: 0.6913 (mmm) REVERT: B 42 ASN cc_start: 0.7564 (t0) cc_final: 0.7047 (t0) REVERT: B 154 MET cc_start: 0.3007 (mmm) cc_final: 0.2364 (mmm) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 1.0421 time to fit residues: 262.4932 Evaluate side-chains 169 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.0980 chunk 235 optimal weight: 40.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 63 ASN O 28 GLN P 63 GLN B 170 HIS ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.182872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.151830 restraints weight = 30445.856| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 0.60 r_work: 0.3066 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 36050 Z= 0.141 Angle : 0.546 8.358 53766 Z= 0.317 Chirality : 0.038 0.317 6842 Planarity : 0.005 0.053 3002 Dihedral : 23.261 177.204 17646 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.12 % Allowed : 15.61 % Favored : 82.27 % 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: 0.47 (0.22), residues: 1406 helix: 1.35 (0.21), residues: 567 sheet: -0.12 (0.32), residues: 246 loop : -0.43 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG T 24 TYR 0.016 0.001 TYR L 117 PHE 0.010 0.001 PHE O 43 TRP 0.011 0.002 TRP P 60 HIS 0.005 0.001 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (36050) covalent geometry : angle 0.54612 / 0.32 (53766) hydrogen bonds : bond 0.06423 / 4.19 ( 1457) hydrogen bonds : angle 3.71377 / 2.65 ( 3057) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.755 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: symmetry clash REVERT: D 68 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8625 (mt) REVERT: D 128 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6610 (mtt-85) REVERT: D 148 LYS cc_start: 0.8116 (tttt) cc_final: 0.7460 (ttpp) REVERT: D 160 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: D 187 GLU cc_start: 0.7309 (pm20) cc_final: 0.7107 (pm20) REVERT: D 197 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7099 (pt0) REVERT: O 35 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7462 (mt0) REVERT: P 76 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8033 (mttp) REVERT: Q 57 ASP cc_start: 0.8286 (m-30) cc_final: 0.7903 (m-30) REVERT: T 3 ASN cc_start: 0.9068 (m-40) cc_final: 0.8868 (m110) REVERT: B 21 ARG cc_start: 0.5089 (OUTLIER) cc_final: 0.4612 (ptt180) REVERT: B 24 ASN cc_start: 0.7098 (t0) cc_final: 0.6736 (t0) REVERT: B 27 MET cc_start: 0.6697 (mmm) cc_final: 0.6399 (mmm) REVERT: B 42 ASN cc_start: 0.7152 (t0) cc_final: 0.6881 (t0) REVERT: B 154 MET cc_start: 0.4030 (mmm) cc_final: 0.3035 (mmm) REVERT: K 84 MET cc_start: 0.6526 (pmt) cc_final: 0.6108 (pmm) outliers start: 25 outliers final: 6 residues processed: 193 average time/residue: 0.9823 time to fit residues: 217.9287 Evaluate side-chains 164 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 187 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [39, 128, 81, 10, 146, 172, 66, 27, 79, 6, 203] chunk 39 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 172 optimal weight: 30.0000 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 203 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN E 70 ASN O 28 GLN B 18 HIS B 203 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.177947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124069 restraints weight = 30002.642| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 0.98 r_work: 0.2962 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 36050 Z= 0.443 Angle : 0.932 12.417 53766 Z= 0.474 Chirality : 0.058 0.428 6842 Planarity : 0.008 0.064 3002 Dihedral : 23.331 178.487 17646 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.31 % Allowed : 15.95 % Favored : 80.75 % 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: 0.06 (0.22), residues: 1406 helix: 0.89 (0.21), residues: 568 sheet: -0.20 (0.32), residues: 240 loop : -0.58 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 8 TYR 0.037 0.003 TYR L 117 PHE 0.021 0.002 PHE Q 37 TRP 0.019 0.003 TRP P 60 HIS 0.012 0.002 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00780 / 0.44 (36050) covalent geometry : angle 0.93233 / 0.47 (53766) hydrogen bonds : bond 0.08204 / 5.50 ( 1457) hydrogen bonds : angle 3.89012 / 2.79 ( 3057) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.756 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 128 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6716 (tmt90) REVERT: D 148 LYS cc_start: 0.8112 (tttt) cc_final: 0.7658 (mptt) REVERT: D 187 GLU cc_start: 0.7525 (pm20) cc_final: 0.7293 (pm20) REVERT: D 197 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7163 (pt0) REVERT: F 90 MET cc_start: 0.6957 (mtp) cc_final: 0.6597 (mtp) REVERT: F 102 MET cc_start: 0.4150 (OUTLIER) cc_final: 0.3463 (pmm) REVERT: L 14 ARG cc_start: 0.7121 (pmm-80) cc_final: 0.6813 (mpt180) REVERT: O 35 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7249 (mt0) REVERT: O 48 LYS cc_start: 0.8369 (mmtp) cc_final: 0.7624 (mtmt) REVERT: O 65 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8397 (mttt) REVERT: P 8 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8867 (ttt90) REVERT: P 76 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8155 (mttp) REVERT: P 77 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7538 (pp20) REVERT: Q 57 ASP cc_start: 0.8308 (m-30) cc_final: 0.7926 (m-30) REVERT: B 93 ASN cc_start: 0.7464 (OUTLIER) cc_final: 0.7236 (p0) REVERT: B 154 MET cc_start: 0.3974 (mmm) cc_final: 0.3162 (mmm) REVERT: B 220 THR cc_start: 0.7209 (t) cc_final: 0.6161 (t) REVERT: B 223 GLU cc_start: 0.8004 (pt0) cc_final: 0.7721 (pp20) outliers start: 39 outliers final: 10 residues processed: 183 average time/residue: 1.0552 time to fit residues: 220.1205 Evaluate side-chains 182 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 222 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [233, 140, 146, 198, 173, 81, 145, 6, 114, 115, 28] chunk 233 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 198 optimal weight: 90.0000 chunk 173 optimal weight: 50.0000 chunk 81 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 114 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.179468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123986 restraints weight = 29850.893| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 0.83 r_work: 0.3017 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36050 Z= 0.249 Angle : 0.676 8.791 53766 Z= 0.366 Chirality : 0.044 0.335 6842 Planarity : 0.006 0.046 3002 Dihedral : 23.205 177.042 17646 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.05 % Allowed : 16.28 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.22), residues: 1406 helix: 1.11 (0.21), residues: 568 sheet: -0.22 (0.32), residues: 243 loop : -0.48 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG T 10 TYR 0.027 0.002 TYR L 117 PHE 0.015 0.002 PHE Q 37 TRP 0.016 0.002 TRP P 60 HIS 0.008 0.001 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.25 (36050) covalent geometry : angle 0.67616 / 0.37 (53766) hydrogen bonds : bond 0.06914 / 4.58 ( 1457) hydrogen bonds : angle 3.66850 / 2.63 ( 3057) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.709 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: symmetry clash revert: symmetry clash REVERT: D 128 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6680 (tmt90) REVERT: D 148 LYS cc_start: 0.8088 (tttt) cc_final: 0.7670 (mptt) REVERT: D 160 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6793 (mt-10) REVERT: D 197 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7118 (pt0) REVERT: F 90 MET cc_start: 0.6828 (mtp) cc_final: 0.6328 (mtp) REVERT: F 102 MET cc_start: 0.4256 (pmm) cc_final: 0.3633 (pmm) REVERT: L 14 ARG cc_start: 0.7060 (pmm-80) cc_final: 0.6741 (mpt180) REVERT: L 20 ASN cc_start: 0.8349 (m-40) cc_final: 0.7939 (p0) REVERT: L 56 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.8188 (ttp-110) REVERT: L 94 ARG cc_start: 0.8580 (mtt180) cc_final: 0.8365 (mtm180) REVERT: O 35 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7220 (mt0) REVERT: O 48 LYS cc_start: 0.8342 (mmtp) cc_final: 0.7589 (mtmt) REVERT: O 65 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8277 (mttt) REVERT: P 76 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8053 (mttp) REVERT: P 77 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7265 (pp20) REVERT: Q 57 ASP cc_start: 0.8233 (m-30) cc_final: 0.7852 (m-30) REVERT: B 20 THR cc_start: 0.3229 (OUTLIER) cc_final: 0.2885 (p) REVERT: B 24 ASN cc_start: 0.6790 (OUTLIER) cc_final: 0.6335 (t0) REVERT: B 93 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7286 (p0) REVERT: B 154 MET cc_start: 0.4096 (mmm) cc_final: 0.3146 (mmm) REVERT: B 220 THR cc_start: 0.7413 (t) cc_final: 0.6467 (t) REVERT: B 223 GLU cc_start: 0.8008 (pt0) cc_final: 0.7699 (pp20) REVERT: K 84 MET cc_start: 0.6296 (OUTLIER) cc_final: 0.5838 (pmt) outliers start: 36 outliers final: 14 residues processed: 187 average time/residue: 0.9484 time to fit residues: 203.1458 Evaluate side-chains 190 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain H residue 114 ARG Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain K residue 84 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [12, 167, 196, 60, 216, 113, 1, 17, 44, 32, 205] chunk 12 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 113 optimal weight: 70.0000 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN D 136 GLN T 3 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.178654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122305 restraints weight = 29893.458| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 0.82 r_work: 0.3008 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 36050 Z= 0.306 Angle : 0.757 9.748 53766 Z= 0.401 Chirality : 0.049 0.375 6842 Planarity : 0.006 0.056 3002 Dihedral : 23.217 177.763 17646 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.56 % Allowed : 16.88 % Favored : 79.56 % 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: 0.17 (0.22), residues: 1406 helix: 1.00 (0.21), residues: 568 sheet: -0.20 (0.32), residues: 243 loop : -0.51 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 77 TYR 0.031 0.003 TYR L 117 PHE 0.016 0.002 PHE Q 37 TRP 0.018 0.002 TRP P 60 HIS 0.010 0.002 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.31 (36050) covalent geometry : angle 0.75662 / 0.40 (53766) hydrogen bonds : bond 0.07453 / 4.99 ( 1457) hydrogen bonds : angle 3.71879 / 2.67 ( 3057) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.839 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 128 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6627 (tmt90) REVERT: D 148 LYS cc_start: 0.8113 (tttt) cc_final: 0.7696 (mptt) REVERT: D 197 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7152 (pt0) REVERT: F 90 MET cc_start: 0.6798 (OUTLIER) cc_final: 0.6183 (mtp) REVERT: F 102 MET cc_start: 0.4165 (pmm) cc_final: 0.3415 (pmm) REVERT: L 14 ARG cc_start: 0.7059 (pmm-80) cc_final: 0.6528 (mpt180) REVERT: L 20 ASN cc_start: 0.8327 (m-40) cc_final: 0.7938 (p0) REVERT: L 56 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.8217 (ttp-110) REVERT: L 94 ARG cc_start: 0.8608 (mtt180) cc_final: 0.8387 (mtm180) REVERT: O 35 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7236 (mt0) REVERT: O 48 LYS cc_start: 0.8378 (mmtp) cc_final: 0.7618 (mtmt) REVERT: O 65 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8324 (mttt) REVERT: P 8 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8843 (ttt90) REVERT: P 76 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8029 (mttp) REVERT: P 77 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7350 (pp20) REVERT: Q 57 ASP cc_start: 0.8246 (m-30) cc_final: 0.7866 (m-30) REVERT: B 24 ASN cc_start: 0.6773 (OUTLIER) cc_final: 0.6311 (t0) REVERT: B 35 ARG cc_start: 0.7523 (tmm160) cc_final: 0.7026 (tmm160) REVERT: B 42 ASN cc_start: 0.7094 (t0) cc_final: 0.6877 (t0) REVERT: B 93 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.7298 (p0) REVERT: B 154 MET cc_start: 0.4423 (mmm) cc_final: 0.3413 (mmm) outliers start: 42 outliers final: 19 residues processed: 185 average time/residue: 1.0057 time to fit residues: 212.8825 Evaluate side-chains 184 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain K residue 84 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [165, 152, 37, 144, 182, 161, 51, 193, 236, 218, 18] chunk 165 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 236 optimal weight: 30.0000 chunk 218 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.178933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118743 restraints weight = 29574.373| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 0.84 r_work: 0.3009 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 36050 Z= 0.356 Angle : 0.812 10.421 53766 Z= 0.424 Chirality : 0.052 0.392 6842 Planarity : 0.007 0.057 3002 Dihedral : 23.226 177.700 17646 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.07 % Allowed : 16.96 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.22), residues: 1406 helix: 0.85 (0.21), residues: 569 sheet: -0.20 (0.32), residues: 245 loop : -0.52 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 77 TYR 0.034 0.003 TYR L 117 PHE 0.018 0.002 PHE Q 37 TRP 0.018 0.002 TRP P 60 HIS 0.011 0.002 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.36 (36050) covalent geometry : angle 0.81242 / 0.42 (53766) hydrogen bonds : bond 0.07632 / 5.11 ( 1457) hydrogen bonds : angle 3.75368 / 2.70 ( 3057) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 0.787 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: symmetry clash REVERT: D 128 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6408 (tmt90) REVERT: D 148 LYS cc_start: 0.8109 (tttt) cc_final: 0.7613 (mptt) REVERT: D 160 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6810 (mt-10) REVERT: D 187 GLU cc_start: 0.7673 (pm20) cc_final: 0.7254 (pm20) REVERT: D 197 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7162 (pt0) REVERT: F 90 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6153 (mtp) REVERT: F 102 MET cc_start: 0.4140 (pmm) cc_final: 0.3286 (pmm) REVERT: H 91 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7282 (mt-10) REVERT: L 14 ARG cc_start: 0.6921 (pmm-80) cc_final: 0.6530 (mpt180) REVERT: L 20 ASN cc_start: 0.8204 (m-40) cc_final: 0.7707 (p0) REVERT: L 56 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.8046 (ttp-110) REVERT: L 94 ARG cc_start: 0.8590 (mtt180) cc_final: 0.8313 (mtm180) REVERT: O 35 GLN cc_start: 0.8119 (mm-40) cc_final: 0.6992 (mt0) REVERT: O 48 LYS cc_start: 0.8346 (mmtp) cc_final: 0.7521 (mtmt) REVERT: O 65 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8184 (mttt) REVERT: P 8 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8808 (ttt90) REVERT: P 76 LYS cc_start: 0.8509 (mtpt) cc_final: 0.7889 (mttp) REVERT: P 77 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7234 (pp20) REVERT: Q 57 ASP cc_start: 0.8268 (m-30) cc_final: 0.7864 (m-30) REVERT: B 24 ASN cc_start: 0.6531 (OUTLIER) cc_final: 0.6099 (t0) REVERT: B 35 ARG cc_start: 0.7563 (tmm160) cc_final: 0.7056 (tmm160) REVERT: B 93 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7302 (p0) REVERT: B 154 MET cc_start: 0.4604 (mmm) cc_final: 0.3606 (mmm) outliers start: 48 outliers final: 23 residues processed: 189 average time/residue: 0.9520 time to fit residues: 206.2128 Evaluate side-chains 189 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain H residue 114 ARG Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain K residue 84 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [160, 232, 112, 223, 113, 123, 239, 176, 86, 85, 235] chunk 160 optimal weight: 5.9990 chunk 232 optimal weight: 40.0000 chunk 112 optimal weight: 30.0000 chunk 223 optimal weight: 8.9990 chunk 113 optimal weight: 70.0000 chunk 123 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 176 optimal weight: 30.0000 chunk 86 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 235 optimal weight: 40.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.177829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.116923 restraints weight = 29686.133| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.00 r_work: 0.2966 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.121 36050 Z= 0.522 Angle : 1.038 12.479 53766 Z= 0.518 Chirality : 0.063 0.460 6842 Planarity : 0.008 0.074 3002 Dihedral : 23.306 178.448 17646 Min Nonbonded Distance : 1.568 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.33 % Allowed : 17.22 % Favored : 78.46 % 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: -0.30 (0.22), residues: 1406 helix: 0.43 (0.21), residues: 575 sheet: -0.18 (0.33), residues: 223 loop : -0.71 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 8 TYR 0.043 0.004 TYR L 117 PHE 0.022 0.003 PHE Q 37 TRP 0.021 0.003 TRP P 60 HIS 0.011 0.002 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00929 / 0.52 (36050) covalent geometry : angle 1.03750 / 0.52 (53766) hydrogen bonds : bond 0.08689 / 5.84 ( 1457) hydrogen bonds : angle 3.93227 / 2.83 ( 3057) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.769 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 34 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7609 (tp) REVERT: D 148 LYS cc_start: 0.8071 (tttt) cc_final: 0.7597 (mptt) REVERT: D 160 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6821 (mt-10) REVERT: D 187 GLU cc_start: 0.7865 (pm20) cc_final: 0.7442 (pm20) REVERT: D 197 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7243 (pt0) REVERT: F 90 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6156 (mtp) REVERT: F 102 MET cc_start: 0.4256 (pmm) cc_final: 0.3343 (pmm) REVERT: H 52 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: H 91 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7588 (mt-10) REVERT: H 117 ARG cc_start: 0.8780 (ttm110) cc_final: 0.8525 (ttm170) REVERT: L 20 ASN cc_start: 0.8323 (m-40) cc_final: 0.7778 (p0) REVERT: L 56 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.8138 (ttp-110) REVERT: L 94 ARG cc_start: 0.8625 (mtt180) cc_final: 0.8341 (mtm180) REVERT: O 35 GLN cc_start: 0.8140 (mm-40) cc_final: 0.6962 (mt0) REVERT: O 48 LYS cc_start: 0.8426 (mmtp) cc_final: 0.7589 (mtmt) REVERT: P 8 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8908 (ttt90) REVERT: P 76 LYS cc_start: 0.8547 (mtpt) cc_final: 0.7947 (mttp) REVERT: P 77 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7327 (pp20) REVERT: Q 57 ASP cc_start: 0.8382 (m-30) cc_final: 0.7988 (m-30) REVERT: B 24 ASN cc_start: 0.6527 (OUTLIER) cc_final: 0.6157 (t0) REVERT: B 35 ARG cc_start: 0.7643 (tmm160) cc_final: 0.7142 (tmm160) REVERT: B 93 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7342 (p0) REVERT: B 154 MET cc_start: 0.4819 (OUTLIER) cc_final: 0.4556 (mmm) outliers start: 51 outliers final: 23 residues processed: 191 average time/residue: 0.9792 time to fit residues: 214.7496 Evaluate side-chains 192 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain K residue 84 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [205, 42, 106, 201, 41, 45, 225, 86, 71, 119, 92] chunk 205 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 201 optimal weight: 40.0000 chunk 41 optimal weight: 0.0980 chunk 45 optimal weight: 0.0870 chunk 225 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 overall best weight: 3.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN Q 51 ASN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.179685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119591 restraints weight = 29658.683| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 0.82 r_work: 0.3026 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 36050 Z= 0.256 Angle : 0.694 9.450 53766 Z= 0.376 Chirality : 0.045 0.341 6842 Planarity : 0.006 0.048 3002 Dihedral : 23.165 178.124 17646 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.99 % Allowed : 17.64 % Favored : 78.37 % 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: 0.05 (0.22), residues: 1406 helix: 0.78 (0.21), residues: 575 sheet: -0.06 (0.33), residues: 238 loop : -0.55 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 77 TYR 0.030 0.002 TYR L 117 PHE 0.015 0.002 PHE Q 37 TRP 0.019 0.002 TRP P 60 HIS 0.008 0.001 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.26 (36050) covalent geometry : angle 0.69386 / 0.38 (53766) hydrogen bonds : bond 0.07079 / 4.72 ( 1457) hydrogen bonds : angle 3.69206 / 2.66 ( 3057) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.777 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: symmetry clash REVERT: D 34 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7534 (tp) REVERT: D 148 LYS cc_start: 0.8064 (tttt) cc_final: 0.7596 (mptt) REVERT: D 160 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6695 (mt-10) REVERT: D 187 GLU cc_start: 0.7778 (pm20) cc_final: 0.7356 (pm20) REVERT: D 197 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7189 (pt0) REVERT: F 90 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6155 (mtp) REVERT: F 102 MET cc_start: 0.4184 (OUTLIER) cc_final: 0.3291 (pmm) REVERT: H 91 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7645 (mt-10) REVERT: H 117 ARG cc_start: 0.8740 (ttm110) cc_final: 0.8490 (ttm170) REVERT: L 14 ARG cc_start: 0.7013 (pmm-80) cc_final: 0.6595 (mpt180) REVERT: L 20 ASN cc_start: 0.8199 (m-40) cc_final: 0.7726 (p0) REVERT: L 56 ARG cc_start: 0.8276 (ttm-80) cc_final: 0.8072 (ttp-110) REVERT: L 94 ARG cc_start: 0.8612 (mtt180) cc_final: 0.8350 (mtm180) REVERT: O 35 GLN cc_start: 0.8107 (mm-40) cc_final: 0.6949 (mt0) REVERT: O 48 LYS cc_start: 0.8335 (mmtp) cc_final: 0.7534 (mtmt) REVERT: P 8 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8726 (ttt90) REVERT: P 76 LYS cc_start: 0.8507 (mtpt) cc_final: 0.7912 (mttp) REVERT: P 77 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7299 (pp20) REVERT: Q 57 ASP cc_start: 0.8288 (m-30) cc_final: 0.7898 (m-30) REVERT: B 35 ARG cc_start: 0.7630 (tmm160) cc_final: 0.7128 (tmm160) REVERT: B 93 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7377 (p0) REVERT: B 154 MET cc_start: 0.4854 (OUTLIER) cc_final: 0.4580 (mmm) REVERT: B 204 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6617 (m-30) outliers start: 47 outliers final: 24 residues processed: 193 average time/residue: 0.9620 time to fit residues: 213.4205 Evaluate side-chains 194 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain H residue 114 ARG Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain K residue 84 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [173, 116, 23, 103, 101, 212, 121, 153, 86, 181, 233] chunk 173 optimal weight: 60.0000 chunk 116 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 233 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.178407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118109 restraints weight = 29607.992| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 0.84 r_work: 0.3006 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 36050 Z= 0.397 Angle : 0.871 10.905 53766 Z= 0.448 Chirality : 0.054 0.409 6842 Planarity : 0.007 0.062 3002 Dihedral : 23.210 179.077 17646 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.56 % Allowed : 18.24 % Favored : 78.20 % 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: -0.08 (0.22), residues: 1406 helix: 0.64 (0.21), residues: 575 sheet: -0.02 (0.33), residues: 223 loop : -0.64 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 8 TYR 0.037 0.003 TYR L 117 PHE 0.019 0.002 PHE Q 37 TRP 0.019 0.002 TRP P 60 HIS 0.011 0.002 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.40 (36050) covalent geometry : angle 0.87092 / 0.45 (53766) hydrogen bonds : bond 0.07850 / 5.27 ( 1457) hydrogen bonds : angle 3.81547 / 2.75 ( 3057) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.512 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 28 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6870 (pp) REVERT: D 34 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7679 (tp) REVERT: D 148 LYS cc_start: 0.8071 (tttt) cc_final: 0.7599 (mptt) REVERT: D 160 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6778 (mt-10) REVERT: D 187 GLU cc_start: 0.7844 (pm20) cc_final: 0.7438 (pm20) REVERT: D 197 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7215 (pt0) REVERT: F 90 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.5922 (mtp) REVERT: F 102 MET cc_start: 0.4285 (OUTLIER) cc_final: 0.3386 (pmm) REVERT: H 52 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: H 91 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7529 (mt-10) REVERT: H 117 ARG cc_start: 0.8781 (ttm110) cc_final: 0.8564 (ttm-80) REVERT: L 14 ARG cc_start: 0.6966 (pmm-80) cc_final: 0.6544 (mpt180) REVERT: L 20 ASN cc_start: 0.8227 (m-40) cc_final: 0.7728 (p0) REVERT: L 56 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.8085 (ttp-110) REVERT: L 94 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8337 (mtm180) REVERT: O 35 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7014 (mt0) REVERT: O 48 LYS cc_start: 0.8350 (mmtp) cc_final: 0.7539 (mtmt) REVERT: P 8 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8909 (ttt90) REVERT: P 76 LYS cc_start: 0.8517 (mtpt) cc_final: 0.7886 (mttp) REVERT: P 77 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7362 (pp20) REVERT: Q 57 ASP cc_start: 0.8291 (m-30) cc_final: 0.7898 (m-30) REVERT: Q 63 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: B 35 ARG cc_start: 0.7677 (tmm160) cc_final: 0.7192 (tmm160) REVERT: B 93 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7440 (p0) REVERT: B 154 MET cc_start: 0.5033 (OUTLIER) cc_final: 0.4720 (mmm) outliers start: 42 outliers final: 25 residues processed: 185 average time/residue: 0.9905 time to fit residues: 210.1693 Evaluate side-chains 195 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain K residue 84 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [156, 59, 174, 185, 118, 90, 2, 80, 61, 143, 198] chunk 156 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 174 optimal weight: 50.0000 chunk 185 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 0.0270 chunk 143 optimal weight: 3.9990 chunk 198 optimal weight: 90.0000 overall best weight: 1.3640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.182030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122704 restraints weight = 30005.984| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 0.81 r_work: 0.3081 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36050 Z= 0.148 Angle : 0.556 9.522 53766 Z= 0.318 Chirality : 0.038 0.309 6842 Planarity : 0.005 0.039 3002 Dihedral : 23.059 178.568 17646 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.71 % Allowed : 19.25 % Favored : 78.03 % 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: 1406 helix: 1.07 (0.21), residues: 576 sheet: 0.09 (0.33), residues: 232 loop : -0.47 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 77 TYR 0.020 0.002 TYR L 117 PHE 0.013 0.001 PHE O 43 TRP 0.016 0.001 TRP P 60 HIS 0.005 0.001 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (36050) covalent geometry : angle 0.55618 / 0.32 (53766) hydrogen bonds : bond 0.06117 / 4.03 ( 1457) hydrogen bonds : angle 3.55509 / 2.56 ( 3057) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.674 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: symmetry clash REVERT: D 28 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6674 (pp) REVERT: D 148 LYS cc_start: 0.8061 (tttt) cc_final: 0.7579 (mptt) REVERT: D 187 GLU cc_start: 0.7734 (pm20) cc_final: 0.7275 (pm20) REVERT: D 197 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7153 (pt0) REVERT: F 90 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6050 (mtp) REVERT: F 102 MET cc_start: 0.4193 (OUTLIER) cc_final: 0.3362 (pmm) REVERT: H 117 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8540 (ttm-80) REVERT: L 20 ASN cc_start: 0.8090 (m-40) cc_final: 0.7632 (p0) REVERT: L 56 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.8026 (ttp-110) REVERT: L 94 ARG cc_start: 0.8586 (mtt180) cc_final: 0.8332 (mtm180) REVERT: O 35 GLN cc_start: 0.8062 (mm-40) cc_final: 0.6917 (mt0) REVERT: P 8 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8669 (ttt90) REVERT: P 76 LYS cc_start: 0.8449 (mtpt) cc_final: 0.7811 (mttp) REVERT: Q 57 ASP cc_start: 0.8264 (m-30) cc_final: 0.7865 (m-30) REVERT: Q 63 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: B 35 ARG cc_start: 0.7681 (tmm160) cc_final: 0.7182 (tmm160) REVERT: B 93 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7432 (p0) REVERT: B 154 MET cc_start: 0.4926 (OUTLIER) cc_final: 0.4636 (mmm) REVERT: B 204 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6587 (m-30) outliers start: 32 outliers final: 18 residues processed: 181 average time/residue: 1.0070 time to fit residues: 209.5915 Evaluate side-chains 187 residues out of total 1179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain K residue 84 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [187, 99, 145, 132, 233, 199, 168, 94, 110, 212, 160] chunk 187 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 199 optimal weight: 50.0000 chunk 168 optimal weight: 10.9990 chunk 94 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN T 3 ASN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.178789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118086 restraints weight = 29465.330| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 0.84 r_work: 0.3008 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 36050 Z= 0.369 Angle : 0.825 10.770 53766 Z= 0.428 Chirality : 0.052 0.393 6842 Planarity : 0.007 0.060 3002 Dihedral : 23.157 179.604 17646 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.14 % Allowed : 18.74 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.22), residues: 1406 helix: 0.81 (0.21), residues: 575 sheet: 0.06 (0.33), residues: 233 loop : -0.53 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 77 TYR 0.036 0.003 TYR L 117 PHE 0.019 0.002 PHE Q 37 TRP 0.018 0.002 TRP P 60 HIS 0.012 0.002 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.37 (36050) covalent geometry : angle 0.82494 / 0.43 (53766) hydrogen bonds : bond 0.07546 / 5.07 ( 1457) hydrogen bonds : angle 3.75195 / 2.70 ( 3057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17512.32 seconds wall clock time: 297 minutes 36.92 seconds (17856.92 seconds total)