Starting phenix.real_space_refine on Thu Oct 29 13:39:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bod_12239/10_2026/7bod_12239.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bod_12239/10_2026/7bod_12239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bod_12239/10_2026/7bod_12239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bod_12239/10_2026/7bod_12239.map" model { file = "/net/cci-nas-00/data/ceres_data/7bod_12239/10_2026/7bod_12239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bod_12239/10_2026/7bod_12239.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7bod_12239/10_2026/7bod_12239.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bod_12239/10_2026/7bod_12239.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1078 5.49 5 Mg 101 5.21 5 S 41 5.16 5 C 16650 2.51 5 N 6220 2.21 5 O 9299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33389 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 23172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 23172 Classifications: {'RNA': 7, 'RNAv2': 1071} Modifications used: {'rna2p': 1, 'rna2p_pur': 77, 'rna2p_pyr': 52, 'rna3p': 7, 'rna3p_pur': 544, 'rna3p_pyr': 397} Link IDs: {'rna2p': 130, 'rna3p': 947} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 5 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 430 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Unusual residues: {' MG': 101} Classifications: {'undetermined': 101} Link IDs: {None: 100} Time building chain proxies: 5.95, per 1000 atoms: 0.18 Number of scatterers: 33389 At special positions: 0 Unit cell: (179.55, 148.05, 177.45, 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 41 16.00 P 1078 15.00 Mg 101 11.99 O 9299 8.00 N 6220 7.00 C 16650 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 619.0 milliseconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 42.5% alpha, 20.3% beta 347 base pairs and 655 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'D' and resid 8 through 16 removed outlier: 3.792A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 31 Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.764A pdb=" N TYR D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 95 removed outlier: 3.543A pdb=" N LEU D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 106 Processing helix chain 'D' and resid 112 through 120 removed outlier: 4.133A pdb=" N VAL D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 150 Processing helix chain 'D' and resid 152 through 162 removed outlier: 3.807A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.745A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 147 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 removed outlier: 3.618A pdb=" N ILE E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 165 " --> pdb=" O VAL E 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 160 through 165' Processing helix chain 'F' and resid 11 through 15 Processing helix chain 'F' and resid 16 through 32 removed outlier: 4.610A pdb=" N GLY F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.545A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.524A pdb=" N LEU H 92 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'K' and resid 59 through 75 Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'K' and resid 94 through 102 removed outlier: 3.518A pdb=" N ALA K 102 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.734A pdb=" N GLN O 40 " --> pdb=" O ILE O 36 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 4.057A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.543A pdb=" N TYR O 78 " --> pdb=" O ASP O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'Q' and resid 49 through 52 removed outlier: 4.139A 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 11 through 16 removed outlier: 3.610A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 Processing helix chain 'R' and resid 31 through 33 No H-bonds generated for 'chain 'R' and resid 31 through 33' Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 65 removed outlier: 3.677A pdb=" N GLN R 54 " --> pdb=" O LYS R 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 39 removed outlier: 3.632A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 64 removed outlier: 3.877A pdb=" N ASN T 52 " --> pdb=" O GLN T 48 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU T 53 " --> pdb=" O LYS T 49 " (cutoff:3.500A) Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 85 Processing helix chain 'U' and resid 12 through 17 Processing helix chain 'U' and resid 18 through 26 removed outlier: 3.633A pdb=" N SER U 22 " --> pdb=" O ARG U 18 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU U 24 " --> pdb=" O LYS U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 27 through 35 removed outlier: 3.509A pdb=" N ARG U 33 " --> pdb=" O LEU U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 58 Processing sheet with id=AA1, first strand: chain 'D' and resid 128 through 129 removed outlier: 4.140A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 12 through 23 removed outlier: 5.102A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.649A 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: 6.743A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 35 through 45 removed outlier: 5.510A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG F 38 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG F 44 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA F 57 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG F 2 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET F 88 " --> pdb=" O VAL F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.642A 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: 5.707A pdb=" N ILE H 125 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 41 through 46 removed outlier: 7.593A pdb=" N GLY K 19 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N MET K 85 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA K 21 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LYS K 87 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE K 23 " --> pdb=" O LYS K 87 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU K 82 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN K 109 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 29 through 40 removed outlier: 5.943A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N TYR L 95 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR L 64 " --> pdb=" O TYR L 95 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N THR L 97 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR L 66 " --> pdb=" O THR L 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 50 through 52 removed outlier: 6.502A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 6.851A 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 14 removed outlier: 7.053A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N LYS Q 71 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N HIS Q 45 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS Q 71 " --> pdb=" O LEU Q 67 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N TRP Q 73 " --> pdb=" O ARG Q 65 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ARG Q 65 " --> pdb=" O TRP Q 73 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N LEU Q 75 " --> pdb=" O GLU Q 63 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLU Q 63 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ARG Q 77 " --> pdb=" O ILE Q 61 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE Q 61 " --> pdb=" O ARG Q 77 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL Q 79 " --> pdb=" O VAL Q 59 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL Q 59 " --> pdb=" O VAL Q 79 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 857 hydrogen bonds 1340 hydrogen bond angles 0 basepair planarities 347 basepair parallelities 655 stacking parallelities Total time for adding SS restraints: 14.34 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3238 1.31 - 1.44: 16089 1.44 - 1.56: 14658 1.56 - 1.69: 2154 1.69 - 1.82: 70 Bond restraints: 36209 Sorted by residual: bond pdb=" N3 G7M A 527 " pdb=" C4 G7M A 527 " ideal model delta sigma weight residual 1.330 1.484 -0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" C2 G7M A 527 " pdb=" N3 G7M A 527 " ideal model delta sigma weight residual 1.317 1.454 -0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" C2 G7M A 527 " pdb=" N2 G7M A 527 " ideal model delta sigma weight residual 1.329 1.448 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C5 G7M A 527 " pdb=" C6 G7M A 527 " ideal model delta sigma weight residual 1.425 1.535 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" N ILE K 116 " pdb=" CA ILE K 116 " ideal model delta sigma weight residual 1.456 1.495 -0.039 8.60e-03 1.35e+04 2.11e+01 ... (remaining 36204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 52114 2.79 - 5.59: 2046 5.59 - 8.38: 46 8.38 - 11.18: 7 11.18 - 13.97: 2 Bond angle restraints: 54215 Sorted by residual: angle pdb=" CA GLY H 109 " pdb=" C GLY H 109 " pdb=" O GLY H 109 " ideal model delta sigma weight residual 122.45 118.23 4.22 7.20e-01 1.93e+00 3.44e+01 angle pdb=" CA GLY D 39 " pdb=" C GLY D 39 " pdb=" O GLY D 39 " ideal model delta sigma weight residual 122.52 118.29 4.23 7.90e-01 1.60e+00 2.87e+01 angle pdb=" N LYS P 46 " pdb=" CA LYS P 46 " pdb=" C LYS P 46 " ideal model delta sigma weight residual 113.17 106.66 6.51 1.26e+00 6.30e-01 2.67e+01 angle pdb=" CA GLY H 53 " pdb=" C GLY H 53 " pdb=" O GLY H 53 " ideal model delta sigma weight residual 122.29 118.26 4.03 8.10e-01 1.52e+00 2.48e+01 angle pdb=" N GLY H 68 " pdb=" CA GLY H 68 " pdb=" C GLY H 68 " ideal model delta sigma weight residual 115.32 108.51 6.81 1.38e+00 5.25e-01 2.44e+01 ... (remaining 54210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.06: 17157 33.06 - 66.12: 2018 66.12 - 99.18: 169 99.18 - 132.24: 3 132.24 - 165.30: 1 Dihedral angle restraints: 19348 sinusoidal: 15648 harmonic: 3700 Sorted by residual: dihedral pdb=" C4' G A 818 " pdb=" C3' G A 818 " pdb=" C2' G A 818 " pdb=" C1' G A 818 " ideal model delta sinusoidal sigma weight residual 36.34 -38.84 75.19 1 3.10e+00 1.04e-01 7.44e+02 dihedral pdb=" C4' G A 413 " pdb=" C3' G A 413 " pdb=" C2' G A 413 " pdb=" C1' G A 413 " ideal model delta sinusoidal sigma weight residual 36.35 -38.70 75.05 1 3.10e+00 1.04e-01 7.41e+02 dihedral pdb=" C4' A A 246 " pdb=" C3' A A 246 " pdb=" C2' A A 246 " pdb=" C1' A A 246 " ideal model delta sinusoidal sigma weight residual 36.35 -38.58 74.92 1 3.10e+00 1.04e-01 7.39e+02 ... (remaining 19345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4954 0.067 - 0.134: 495 0.134 - 0.201: 297 0.201 - 0.268: 1027 0.268 - 0.335: 146 Chirality restraints: 6919 Sorted by residual: chirality pdb=" CB D2T L 89 " pdb=" CA D2T L 89 " pdb=" SB D2T L 89 " pdb=" CG D2T L 89 " both_signs ideal model delta sigma weight residual False -3.02 -3.35 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" P U A 686 " pdb=" OP1 U A 686 " pdb=" OP2 U A 686 " pdb=" O5' U A 686 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C3' G A 733 " pdb=" C4' G A 733 " pdb=" O3' G A 733 " pdb=" C2' G A 733 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 6916 not shown) Planarity restraints: 2864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1518 " 0.126 2.00e-02 2.50e+03 2.08e-01 4.31e+02 pdb=" N6 MA6 A1518 " -0.360 2.00e-02 2.50e+03 pdb=" C10 MA6 A1518 " 0.119 2.00e-02 2.50e+03 pdb=" C9 MA6 A1518 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " 0.117 2.00e-02 2.50e+03 1.94e-01 3.77e+02 pdb=" N6 MA6 A1519 " -0.336 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " 0.112 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY L 85 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C GLY L 85 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY L 85 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG L 86 " 0.015 2.00e-02 2.50e+03 ... (remaining 2861 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 197 2.51 - 3.11: 22299 3.11 - 3.71: 63386 3.71 - 4.30: 97737 4.30 - 4.90: 127862 Nonbonded interactions: 311481 Sorted by model distance: nonbonded pdb=" OP1 C A 770 " pdb="MG MG A1689 " model vdw 1.913 2.170 nonbonded pdb=" OP1 A A 59 " pdb="MG MG A1623 " model vdw 1.965 2.170 nonbonded pdb=" O LYS O 73 " pdb=" OD1 ASP O 74 " model vdw 1.983 3.040 nonbonded pdb=" OP1 G A 558 " pdb="MG MG A1633 " model vdw 1.985 2.170 nonbonded pdb=" OP2 G A 289 " pdb="MG MG A1687 " model vdw 1.999 2.170 ... (remaining 311476 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 38.520 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.667 36211 Z= 0.540 Angle : 1.033 13.972 54215 Z= 0.519 Chirality : 0.110 0.335 6919 Planarity : 0.007 0.208 2864 Dihedral : 20.428 165.296 16958 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.47 % Allowed : 3.78 % Favored : 95.75 % 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: -1.72 (0.21), residues: 1262 helix: -1.26 (0.21), residues: 488 sheet: -0.88 (0.33), residues: 224 loop : -0.94 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG T 10 TYR 0.016 0.002 TYR Q 34 PHE 0.014 0.002 PHE O 43 TRP 0.010 0.002 TRP K 44 HIS 0.010 0.001 HIS R 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.41 (36209) covalent geometry : angle 1.03303 / 0.52 (54215) hydrogen bonds : bond 0.20804 / 10.77 ( 1327) hydrogen bonds : angle 7.37113 / 2.91 ( 2687) Misc. bond : bond 0.47137 / 23.57 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 450 time to evaluate : 0.598 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 178 MET cc_start: 0.7321 (mtt) cc_final: 0.7105 (mtt) REVERT: E 73 ASN cc_start: 0.7600 (m-40) cc_final: 0.7331 (m-40) REVERT: F 52 ASN cc_start: 0.7605 (t0) cc_final: 0.7385 (t160) REVERT: F 93 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7687 (ttmm) outliers start: 5 outliers final: 3 residues processed: 454 average time/residue: 0.8098 time to fit residues: 426.9871 Evaluate side-chains 352 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 349 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain H residue 14 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 200] chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 36 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN D 126 ASN E 82 GLN E 83 HIS E 89 HIS E 135 ASN E 146 ASN E 148 ASN H 18 GLN K 40 ASN K 81 ASN K 101 ASN L 6 GLN L 96 HIS O 20 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 HIS O 40 GLN O 80 GLN P 26 ASN P 29 ASN P 59 HIS T 20 HIS T 61 GLN T 78 ASN T 84 ASN U 56 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.067739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.049745 restraints weight = 91794.540| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 1.14 r_work: 0.2619 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9136 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 36211 Z= 0.383 Angle : 1.316 19.797 54215 Z= 0.529 Chirality : 0.112 1.330 6919 Planarity : 0.006 0.057 2864 Dihedral : 19.065 174.940 14417 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.73 % Allowed : 19.66 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.22), residues: 1262 helix: -0.25 (0.22), residues: 506 sheet: -0.65 (0.33), residues: 239 loop : -0.37 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 11 TYR 0.015 0.002 TYR R 64 PHE 0.020 0.002 PHE F 8 TRP 0.017 0.002 TRP P 60 HIS 0.007 0.002 HIS D 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00780 / 0.38 (36209) covalent geometry : angle 1.31633 / 0.53 (54215) hydrogen bonds : bond 0.06650 / 3.48 ( 1327) hydrogen bonds : angle 3.75990 / 1.48 ( 2687) Misc. bond : bond 0.00554 / 0.28 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 361 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 43 ASN cc_start: 0.8786 (t0) cc_final: 0.8549 (t0) REVERT: F 78 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8740 (m-80) REVERT: F 90 MET cc_start: 0.8350 (mtp) cc_final: 0.8012 (mtp) REVERT: H 5 ASP cc_start: 0.8367 (t0) cc_final: 0.8127 (t70) REVERT: H 38 ASN cc_start: 0.8320 (t0) cc_final: 0.8073 (t0) REVERT: K 85 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7758 (mmm) REVERT: K 110 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8659 (mp) REVERT: O 40 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8453 (mm110) REVERT: U 18 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.4929 (mtp180) REVERT: U 19 PHE cc_start: 0.8308 (t80) cc_final: 0.7701 (t80) REVERT: U 54 LYS cc_start: 0.8597 (tmmm) cc_final: 0.8318 (tmmt) outliers start: 50 outliers final: 26 residues processed: 384 average time/residue: 0.7731 time to fit residues: 346.8398 Evaluate side-chains 368 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 338 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 18 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [210, 104, 28, 176, 45, 115, 128, 154, 83, 88, 171] chunk 210 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 115 optimal weight: 0.0370 chunk 128 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN F 52 ASN H 18 GLN L 5 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN P 26 ASN U 56 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.069156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.051278 restraints weight = 91300.364| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.08 r_work: 0.2664 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 36211 Z= 0.291 Angle : 1.121 15.462 54215 Z= 0.456 Chirality : 0.093 1.166 6919 Planarity : 0.005 0.058 2864 Dihedral : 19.197 179.784 14417 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 6.43 % Allowed : 20.89 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.23), residues: 1262 helix: 0.32 (0.23), residues: 503 sheet: -0.62 (0.35), residues: 227 loop : -0.22 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 55 TYR 0.013 0.002 TYR R 64 PHE 0.014 0.001 PHE O 43 TRP 0.009 0.002 TRP K 44 HIS 0.004 0.001 HIS L 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.29 (36209) covalent geometry : angle 1.12125 / 0.46 (54215) hydrogen bonds : bond 0.05720 / 3.02 ( 1327) hydrogen bonds : angle 3.47015 / 1.37 ( 2687) Misc. bond : bond 0.00441 / 0.22 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 359 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 43 ASN cc_start: 0.8845 (t0) cc_final: 0.8620 (t0) REVERT: E 64 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8804 (mmt) REVERT: E 142 ASP cc_start: 0.8726 (t0) cc_final: 0.8504 (t0) REVERT: F 74 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9253 (tt) REVERT: F 78 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8709 (m-80) REVERT: H 5 ASP cc_start: 0.8355 (t0) cc_final: 0.8071 (t70) REVERT: H 118 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8062 (tp40) REVERT: K 85 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7740 (mmm) REVERT: K 110 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8639 (mm) REVERT: P 31 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8706 (ttp-170) REVERT: Q 38 ILE cc_start: 0.9340 (pt) cc_final: 0.9058 (mm) REVERT: T 48 GLN cc_start: 0.9048 (tp-100) cc_final: 0.8671 (tp-100) REVERT: T 60 ARG cc_start: 0.9481 (OUTLIER) cc_final: 0.8713 (ttp80) REVERT: U 18 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.4138 (tmt170) REVERT: U 54 LYS cc_start: 0.8553 (tmmm) cc_final: 0.8227 (tmmt) outliers start: 68 outliers final: 29 residues processed: 386 average time/residue: 0.7746 time to fit residues: 349.2645 Evaluate side-chains 387 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 349 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 80 LYS Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain U residue 18 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [153, 118, 70, 49, 204, 103, 46, 114, 164, 86, 161] chunk 153 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 161 optimal weight: 0.5980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 146 ASN F 52 ASN L 5 ASN O 20 ASN O 40 GLN O 80 GLN P 26 ASN U 56 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.069654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.051843 restraints weight = 90785.414| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.08 r_work: 0.2680 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 36211 Z= 0.254 Angle : 1.084 15.211 54215 Z= 0.441 Chirality : 0.090 1.108 6919 Planarity : 0.005 0.061 2864 Dihedral : 19.135 179.268 14415 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.95 % Allowed : 23.06 % Favored : 70.98 % 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: 0.02 (0.23), residues: 1262 helix: 0.63 (0.23), residues: 505 sheet: -0.53 (0.34), residues: 227 loop : -0.16 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 11 TYR 0.010 0.002 TYR L 95 PHE 0.014 0.001 PHE K 52 TRP 0.008 0.002 TRP F 42 HIS 0.003 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.25 (36209) covalent geometry : angle 1.08443 / 0.44 (54215) hydrogen bonds : bond 0.05575 / 2.94 ( 1327) hydrogen bonds : angle 3.33159 / 1.31 ( 2687) Misc. bond : bond 0.00413 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 359 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 178 MET cc_start: 0.8767 (mtt) cc_final: 0.8540 (mtt) REVERT: E 146 ASN cc_start: 0.8242 (m-40) cc_final: 0.8007 (m110) REVERT: F 35 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8484 (mmtm) REVERT: F 74 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9175 (tt) REVERT: F 78 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8551 (m-80) REVERT: H 5 ASP cc_start: 0.8367 (t0) cc_final: 0.8077 (t70) REVERT: H 118 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7999 (tp40) REVERT: K 52 PHE cc_start: 0.8465 (m-80) cc_final: 0.8224 (m-80) REVERT: K 85 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7604 (mmm) REVERT: K 110 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8409 (mm) REVERT: O 14 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8218 (tm-30) REVERT: P 31 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8661 (ttp-170) REVERT: T 48 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8672 (tp-100) REVERT: T 60 ARG cc_start: 0.9496 (OUTLIER) cc_final: 0.8749 (ttp80) REVERT: U 18 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.4201 (tmt170) REVERT: U 19 PHE cc_start: 0.8248 (t80) cc_final: 0.7799 (t80) REVERT: U 21 ARG cc_start: 0.8374 (mpt180) cc_final: 0.8095 (mpt180) REVERT: U 54 LYS cc_start: 0.8513 (tmmm) cc_final: 0.8229 (tmmt) outliers start: 63 outliers final: 36 residues processed: 386 average time/residue: 0.7713 time to fit residues: 348.1907 Evaluate side-chains 392 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 348 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain U residue 18 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [199, 53, 23, 155, 179, 157, 87, 66, 144, 59, 21] chunk 199 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 179 optimal weight: 0.0010 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN L 5 ASN O 20 ASN O 40 GLN O 80 GLN P 26 ASN U 56 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.069529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.051717 restraints weight = 91248.186| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.07 r_work: 0.2674 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36211 Z= 0.262 Angle : 1.077 15.270 54215 Z= 0.438 Chirality : 0.089 1.055 6919 Planarity : 0.005 0.057 2864 Dihedral : 19.134 179.625 14415 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 6.24 % Allowed : 24.10 % Favored : 69.66 % 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: 0.15 (0.23), residues: 1262 helix: 0.85 (0.23), residues: 504 sheet: -0.53 (0.34), residues: 226 loop : -0.17 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 34 TYR 0.015 0.002 TYR R 32 PHE 0.023 0.002 PHE U 12 TRP 0.012 0.002 TRP F 42 HIS 0.005 0.001 HIS O 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.26 (36209) covalent geometry : angle 1.07738 / 0.44 (54215) hydrogen bonds : bond 0.05534 / 2.92 ( 1327) hydrogen bonds : angle 3.29723 / 1.29 ( 2687) Misc. bond : bond 0.00420 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 350 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 178 MET cc_start: 0.8764 (mtt) cc_final: 0.8512 (mtt) REVERT: E 43 ASN cc_start: 0.8918 (t0) cc_final: 0.8680 (t0) REVERT: E 146 ASN cc_start: 0.8255 (m-40) cc_final: 0.7987 (m110) REVERT: E 159 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8720 (ptpt) REVERT: F 74 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9354 (tm) REVERT: F 75 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8527 (tm-30) REVERT: F 78 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: F 91 ARG cc_start: 0.8775 (mtp180) cc_final: 0.8506 (mtp-110) REVERT: H 5 ASP cc_start: 0.8370 (t0) cc_final: 0.8078 (t70) REVERT: H 118 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7986 (tp40) REVERT: K 52 PHE cc_start: 0.8514 (m-80) cc_final: 0.8231 (m-80) REVERT: K 85 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7598 (mmm) REVERT: K 110 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8413 (mm) REVERT: O 14 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8250 (tm-30) REVERT: O 20 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.8024 (t0) REVERT: P 31 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8689 (ttp-170) REVERT: T 43 ASP cc_start: 0.8117 (t0) cc_final: 0.7657 (p0) REVERT: T 60 ARG cc_start: 0.9491 (OUTLIER) cc_final: 0.8750 (ttp80) REVERT: U 18 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.4301 (tmt170) REVERT: U 19 PHE cc_start: 0.8249 (t80) cc_final: 0.7785 (t80) REVERT: U 21 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8115 (mpt180) REVERT: U 45 ARG cc_start: 0.8607 (mtm-85) cc_final: 0.8384 (mtm-85) REVERT: U 54 LYS cc_start: 0.8506 (tmmm) cc_final: 0.8237 (tmmt) outliers start: 66 outliers final: 37 residues processed: 380 average time/residue: 0.7564 time to fit residues: 336.7882 Evaluate side-chains 385 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 338 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain O residue 20 ASN Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 21 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [178, 222, 35, 96, 183, 173, 163, 127, 214, 153, 162] chunk 178 optimal weight: 9.9990 chunk 222 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 183 optimal weight: 0.5980 chunk 173 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN F 52 ASN L 5 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN P 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.071008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.053427 restraints weight = 90651.792| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.09 r_work: 0.2723 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 36211 Z= 0.187 Angle : 1.040 14.767 54215 Z= 0.423 Chirality : 0.085 0.970 6919 Planarity : 0.005 0.060 2864 Dihedral : 19.143 179.840 14414 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.01 % Allowed : 25.99 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.23), residues: 1262 helix: 1.00 (0.23), residues: 507 sheet: -0.44 (0.34), residues: 224 loop : -0.15 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 6 TYR 0.009 0.001 TYR L 95 PHE 0.017 0.002 PHE U 12 TRP 0.013 0.002 TRP F 42 HIS 0.003 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 (36209) covalent geometry : angle 1.03979 / 0.42 (54215) hydrogen bonds : bond 0.05479 / 2.89 ( 1327) hydrogen bonds : angle 3.21589 / 1.26 ( 2687) Misc. bond : bond 0.00351 / 0.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 360 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 MET cc_start: 0.8768 (mtt) cc_final: 0.8499 (mtt) REVERT: E 43 ASN cc_start: 0.8933 (t0) cc_final: 0.8674 (t0) REVERT: E 146 ASN cc_start: 0.8258 (m-40) cc_final: 0.8018 (m110) REVERT: F 35 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8615 (mmtt) REVERT: F 74 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9343 (tt) REVERT: F 75 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8472 (tm-30) REVERT: F 78 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8646 (m-80) REVERT: F 81 ASN cc_start: 0.8589 (t0) cc_final: 0.8297 (t0) REVERT: F 90 MET cc_start: 0.8327 (mtp) cc_final: 0.8106 (mtp) REVERT: F 91 ARG cc_start: 0.8759 (mtp180) cc_final: 0.8493 (mtp-110) REVERT: H 5 ASP cc_start: 0.8372 (t0) cc_final: 0.8082 (t70) REVERT: H 118 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7973 (tp40) REVERT: K 52 PHE cc_start: 0.8458 (m-80) cc_final: 0.8169 (m-80) REVERT: K 82 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7577 (pp) REVERT: K 85 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7580 (mmm) REVERT: K 110 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8445 (mp) REVERT: L 111 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8818 (mtpt) REVERT: O 14 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8284 (tm-30) REVERT: O 20 ASN cc_start: 0.8230 (t0) cc_final: 0.7992 (t0) REVERT: O 40 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8344 (mm110) REVERT: T 43 ASP cc_start: 0.8010 (t0) cc_final: 0.7540 (p0) REVERT: T 60 ARG cc_start: 0.9474 (OUTLIER) cc_final: 0.8717 (ttp80) REVERT: U 18 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.4228 (tmt170) REVERT: U 21 ARG cc_start: 0.8349 (mpt180) cc_final: 0.8114 (mpt180) REVERT: U 45 ARG cc_start: 0.8662 (mtm-85) cc_final: 0.8444 (mtm-85) REVERT: U 54 LYS cc_start: 0.8506 (tmmm) cc_final: 0.8229 (tmmt) outliers start: 53 outliers final: 29 residues processed: 381 average time/residue: 0.7517 time to fit residues: 335.1348 Evaluate side-chains 378 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 340 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 43 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [13, 68, 150, 8, 85, 87, 156, 54, 17, 82, 129] chunk 13 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 150 optimal weight: 0.0870 chunk 8 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 overall best weight: 2.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN E 19 ASN E 61 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN K 38 GLN L 5 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN T 48 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.070390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.052680 restraints weight = 91260.346| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.10 r_work: 0.2705 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 36211 Z= 0.235 Angle : 1.052 14.952 54215 Z= 0.429 Chirality : 0.086 0.991 6919 Planarity : 0.005 0.057 2864 Dihedral : 19.058 179.771 14414 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.20 % Allowed : 26.75 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.23), residues: 1262 helix: 1.06 (0.23), residues: 506 sheet: -0.39 (0.34), residues: 224 loop : -0.11 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 6 TYR 0.009 0.001 TYR L 95 PHE 0.016 0.002 PHE R 13 TRP 0.011 0.002 TRP F 42 HIS 0.006 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.23 (36209) covalent geometry : angle 1.05235 / 0.43 (54215) hydrogen bonds : bond 0.05460 / 2.88 ( 1327) hydrogen bonds : angle 3.22365 / 1.27 ( 2687) Misc. bond : bond 0.00396 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 349 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 MET cc_start: 0.8788 (mtt) cc_final: 0.8499 (mtt) REVERT: E 43 ASN cc_start: 0.8943 (t0) cc_final: 0.8522 (t0) REVERT: E 142 ASP cc_start: 0.8644 (t0) cc_final: 0.8383 (t0) REVERT: E 146 ASN cc_start: 0.8271 (m-40) cc_final: 0.7980 (m110) REVERT: F 35 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8582 (mmtt) REVERT: F 46 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8365 (tp40) REVERT: F 75 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8500 (tm-30) REVERT: F 78 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: F 81 ASN cc_start: 0.8714 (t0) cc_final: 0.8370 (t0) REVERT: F 90 MET cc_start: 0.8353 (mtp) cc_final: 0.8056 (mtp) REVERT: F 91 ARG cc_start: 0.8752 (mtp180) cc_final: 0.8506 (mtp-110) REVERT: F 102 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6238 (mtp) REVERT: H 5 ASP cc_start: 0.8384 (t0) cc_final: 0.8112 (t70) REVERT: H 118 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7952 (tp40) REVERT: K 52 PHE cc_start: 0.8516 (m-80) cc_final: 0.8206 (m-80) REVERT: K 82 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7440 (pp) REVERT: K 85 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7450 (mmm) REVERT: L 111 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8824 (mtpt) REVERT: O 14 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8224 (tm-30) REVERT: O 20 ASN cc_start: 0.8319 (t0) cc_final: 0.8057 (t0) REVERT: T 60 ARG cc_start: 0.9480 (OUTLIER) cc_final: 0.8717 (ttp80) REVERT: U 18 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.4169 (tmt170) REVERT: U 21 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8189 (mpt180) REVERT: U 54 LYS cc_start: 0.8516 (tmmm) cc_final: 0.8263 (tmmt) outliers start: 55 outliers final: 33 residues processed: 371 average time/residue: 0.7714 time to fit residues: 335.1074 Evaluate side-chains 385 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 343 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 78 PHE Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 43 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [217, 152, 123, 191, 61, 162, 97, 43, 188, 56, 124] chunk 217 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 14 GLN F 52 ASN F 68 GLN L 5 ASN L 20 ASN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.070701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.053063 restraints weight = 90706.526| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.09 r_work: 0.2712 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 36211 Z= 0.217 Angle : 1.045 14.855 54215 Z= 0.426 Chirality : 0.085 0.973 6919 Planarity : 0.005 0.055 2864 Dihedral : 19.060 179.682 14414 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.91 % Allowed : 27.60 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.23), residues: 1262 helix: 1.11 (0.23), residues: 510 sheet: -0.40 (0.34), residues: 228 loop : -0.10 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 6 TYR 0.009 0.001 TYR L 95 PHE 0.016 0.002 PHE F 78 TRP 0.010 0.002 TRP F 42 HIS 0.007 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (36209) covalent geometry : angle 1.04518 / 0.43 (54215) hydrogen bonds : bond 0.05447 / 2.88 ( 1327) hydrogen bonds : angle 3.21379 / 1.27 ( 2687) Misc. bond : bond 0.00378 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 346 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 178 MET cc_start: 0.8784 (mtt) cc_final: 0.8485 (mtt) REVERT: E 43 ASN cc_start: 0.8946 (t0) cc_final: 0.8531 (t0) REVERT: E 142 ASP cc_start: 0.8634 (t0) cc_final: 0.8362 (t0) REVERT: E 146 ASN cc_start: 0.8267 (m-40) cc_final: 0.7956 (m110) REVERT: E 162 GLU cc_start: 0.7922 (tp30) cc_final: 0.7541 (mm-30) REVERT: F 35 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8572 (mmtt) REVERT: F 46 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8355 (tp40) REVERT: F 75 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8488 (tm-30) REVERT: F 81 ASN cc_start: 0.8711 (t0) cc_final: 0.8369 (t0) REVERT: F 90 MET cc_start: 0.8346 (mtp) cc_final: 0.8067 (mtp) REVERT: F 91 ARG cc_start: 0.8739 (mtp180) cc_final: 0.8510 (mtp-110) REVERT: F 102 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6168 (mtp) REVERT: H 5 ASP cc_start: 0.8379 (t0) cc_final: 0.8114 (t70) REVERT: H 118 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7944 (tp40) REVERT: K 52 PHE cc_start: 0.8540 (m-80) cc_final: 0.8233 (m-80) REVERT: K 82 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7425 (pp) REVERT: K 85 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7500 (mmm) REVERT: K 112 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: L 111 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8833 (mtpt) REVERT: O 14 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8256 (tm-30) REVERT: O 20 ASN cc_start: 0.8358 (t0) cc_final: 0.8106 (t0) REVERT: T 43 ASP cc_start: 0.8135 (t0) cc_final: 0.7755 (p0) REVERT: T 60 ARG cc_start: 0.9477 (OUTLIER) cc_final: 0.8717 (ttp80) REVERT: U 18 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.4161 (tmt170) REVERT: U 19 PHE cc_start: 0.7906 (t80) cc_final: 0.7437 (t80) REVERT: U 21 ARG cc_start: 0.8416 (mpt180) cc_final: 0.8207 (mpt180) REVERT: U 54 LYS cc_start: 0.8417 (tmmm) cc_final: 0.8145 (tmmt) outliers start: 52 outliers final: 36 residues processed: 369 average time/residue: 0.7710 time to fit residues: 333.3915 Evaluate side-chains 385 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 341 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 43 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [193, 11, 177, 227, 213, 36, 111, 198, 17, 31, 163] chunk 193 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 111 optimal weight: 0.0060 chunk 198 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 GLN F 52 ASN F 68 GLN L 5 ASN L 20 ASN O 40 GLN P 26 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.071329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.053749 restraints weight = 90461.697| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.08 r_work: 0.2730 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36211 Z= 0.181 Angle : 1.036 14.639 54215 Z= 0.423 Chirality : 0.084 0.947 6919 Planarity : 0.005 0.057 2864 Dihedral : 19.075 179.712 14414 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.73 % Allowed : 27.69 % Favored : 67.58 % 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: 0.49 (0.23), residues: 1262 helix: 1.15 (0.23), residues: 506 sheet: -0.33 (0.35), residues: 214 loop : -0.05 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 6 TYR 0.009 0.001 TYR L 95 PHE 0.042 0.002 PHE F 78 TRP 0.008 0.001 TRP F 42 HIS 0.010 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (36209) covalent geometry : angle 1.03560 / 0.42 (54215) hydrogen bonds : bond 0.05445 / 2.87 ( 1327) hydrogen bonds : angle 3.20882 / 1.27 ( 2687) Misc. bond : bond 0.00345 / 0.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 346 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 MET cc_start: 0.8785 (mtt) cc_final: 0.8567 (mtt) REVERT: E 13 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7715 (mt-10) REVERT: E 43 ASN cc_start: 0.8948 (t0) cc_final: 0.8495 (t0) REVERT: E 64 MET cc_start: 0.9060 (mmt) cc_final: 0.8749 (mmt) REVERT: E 142 ASP cc_start: 0.8645 (t0) cc_final: 0.8374 (t0) REVERT: E 146 ASN cc_start: 0.8250 (m-40) cc_final: 0.7941 (m110) REVERT: E 162 GLU cc_start: 0.7938 (tp30) cc_final: 0.7578 (mm-30) REVERT: F 46 GLN cc_start: 0.8644 (tp-100) cc_final: 0.8358 (tp40) REVERT: F 75 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8331 (tm-30) REVERT: F 81 ASN cc_start: 0.8697 (t0) cc_final: 0.8348 (t0) REVERT: F 90 MET cc_start: 0.8349 (mtp) cc_final: 0.8069 (mtp) REVERT: F 102 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6140 (mtp) REVERT: H 5 ASP cc_start: 0.8371 (t0) cc_final: 0.8107 (t70) REVERT: H 118 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7934 (tp40) REVERT: K 52 PHE cc_start: 0.8523 (m-80) cc_final: 0.8216 (m-80) REVERT: K 82 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7412 (pp) REVERT: K 85 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7502 (mmm) REVERT: K 112 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8203 (m-30) REVERT: L 111 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8832 (mtpt) REVERT: O 14 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8224 (tm-30) REVERT: O 20 ASN cc_start: 0.8355 (t0) cc_final: 0.8105 (t0) REVERT: T 43 ASP cc_start: 0.8217 (t0) cc_final: 0.7706 (p0) REVERT: T 60 ARG cc_start: 0.9469 (OUTLIER) cc_final: 0.8742 (ttp80) REVERT: U 18 ARG cc_start: 0.6445 (OUTLIER) cc_final: 0.4139 (tmt170) REVERT: U 19 PHE cc_start: 0.7967 (t80) cc_final: 0.7504 (t80) REVERT: U 21 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8029 (mpt180) REVERT: U 54 LYS cc_start: 0.8412 (tmmm) cc_final: 0.8138 (tmmt) outliers start: 50 outliers final: 36 residues processed: 368 average time/residue: 0.7587 time to fit residues: 328.2544 Evaluate side-chains 384 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 339 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 15 ASP Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 43 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [154, 179, 186, 101, 165, 140, 114, 38, 21, 92, 9] chunk 154 optimal weight: 8.9990 chunk 179 optimal weight: 0.1980 chunk 186 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 14 GLN F 52 ASN F 68 GLN K 38 GLN L 5 ASN L 20 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.050645 restraints weight = 91508.449| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 1.09 r_work: 0.2647 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 36211 Z= 0.321 Angle : 1.127 15.643 54215 Z= 0.460 Chirality : 0.092 1.113 6919 Planarity : 0.005 0.057 2864 Dihedral : 19.098 179.610 14414 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.82 % Allowed : 28.17 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1262 helix: 0.98 (0.23), residues: 506 sheet: -0.27 (0.34), residues: 221 loop : -0.06 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 34 TYR 0.011 0.002 TYR L 95 PHE 0.020 0.002 PHE R 13 TRP 0.015 0.002 TRP F 42 HIS 0.006 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.32 (36209) covalent geometry : angle 1.12714 / 0.46 (54215) hydrogen bonds : bond 0.05688 / 3.00 ( 1327) hydrogen bonds : angle 3.31531 / 1.31 ( 2687) Misc. bond : bond 0.00477 / 0.24 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 347 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 142 ASP cc_start: 0.8766 (t0) cc_final: 0.8516 (t0) REVERT: E 146 ASN cc_start: 0.8269 (m-40) cc_final: 0.7977 (m110) REVERT: F 35 LYS cc_start: 0.8850 (mtpp) cc_final: 0.8507 (mmtt) REVERT: F 75 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8410 (tm-30) REVERT: F 81 ASN cc_start: 0.8770 (t0) cc_final: 0.8390 (t0) REVERT: F 102 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6574 (mtp) REVERT: H 5 ASP cc_start: 0.8419 (t0) cc_final: 0.8158 (t70) REVERT: H 118 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7935 (tp40) REVERT: K 52 PHE cc_start: 0.8631 (m-80) cc_final: 0.8348 (m-80) REVERT: K 85 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7430 (mmm) REVERT: K 112 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8269 (m-30) REVERT: L 111 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8846 (mtpt) REVERT: O 14 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8245 (tm-30) REVERT: O 20 ASN cc_start: 0.8444 (t0) cc_final: 0.8174 (t0) REVERT: O 48 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8502 (mtpp) REVERT: Q 81 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8153 (tppt) REVERT: T 43 ASP cc_start: 0.8296 (t0) cc_final: 0.7910 (p0) REVERT: T 60 ARG cc_start: 0.9505 (OUTLIER) cc_final: 0.8705 (ttp80) REVERT: U 18 ARG cc_start: 0.6320 (OUTLIER) cc_final: 0.4067 (tmt170) REVERT: U 19 PHE cc_start: 0.7985 (t80) cc_final: 0.7622 (t80) REVERT: U 21 ARG cc_start: 0.8417 (mpt180) cc_final: 0.8111 (mpt180) REVERT: U 54 LYS cc_start: 0.8423 (tmmm) cc_final: 0.8157 (tmmt) outliers start: 51 outliers final: 34 residues processed: 368 average time/residue: 0.7718 time to fit residues: 330.9768 Evaluate side-chains 383 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 341 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 39 LYS Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 60 ARG Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 43 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: [19, 144, 134, 52, 77, 205, 159, 143, 178, 20, 176] chunk 19 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 205 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 89 HIS F 14 GLN F 68 GLN K 28 ASN L 5 ASN L 20 ASN O 80 GLN P 26 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.049752 restraints weight = 91567.897| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.07 r_work: 0.2624 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 36211 Z= 0.371 Angle : 1.175 15.996 54215 Z= 0.481 Chirality : 0.097 1.185 6919 Planarity : 0.005 0.067 2864 Dihedral : 19.185 178.820 14414 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.63 % Allowed : 28.45 % Favored : 66.92 % 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: 0.28 (0.23), residues: 1262 helix: 0.85 (0.23), residues: 506 sheet: -0.29 (0.35), residues: 215 loop : -0.09 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Q 6 TYR 0.011 0.002 TYR L 95 PHE 0.020 0.002 PHE R 13 TRP 0.013 0.002 TRP F 42 HIS 0.005 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.37 (36209) covalent geometry : angle 1.17497 / 0.48 (54215) hydrogen bonds : bond 0.05808 / 3.05 ( 1327) hydrogen bonds : angle 3.40177 / 1.34 ( 2687) Misc. bond : bond 0.00534 / 0.27 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12055.57 seconds wall clock time: 205 minutes 36.85 seconds (12336.85 seconds total)