Starting phenix.real_space_refine on Tue Sep 15 11:14:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5an9_3145/09_2026/5an9_3145.cif Found real_map, /net/cci-nas-00/data/ceres_data/5an9_3145/09_2026/5an9_3145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5an9_3145/09_2026/5an9_3145.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5an9_3145/09_2026/5an9_3145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5an9_3145/09_2026/5an9_3145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5an9_3145/09_2026/5an9_3145.map" model { file = "/net/cci-nas-00/data/ceres_data/5an9_3145/09_2026/5an9_3145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5an9_3145/09_2026/5an9_3145.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1158 5.49 5 S 85 5.16 5 C 20518 2.51 5 N 7140 2.21 5 O 10792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39693 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3176 Classifications: {'peptide': 398} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 12, 'TRANS': 382} Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1491 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 184} Chain: "C" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1571 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain: "D" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1245 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 151} Chain: "E" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1017 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 6, 'TRANS': 125} Chain: "F" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "G" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 586 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "H" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 427 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "I" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1686 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "J" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2015 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 243} Chain: "N" Number of atoms: 24758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1162, 24758 Classifications: {'RNAv2': 1162} Modifications used: {'rna2p_pur': 108, 'rna2p_pyr': 58, 'rna3p_pur': 516, 'rna3p_pyr': 480} Link IDs: {'rna2p': 166, 'rna3p': 995} Unresolved chain links: 3 Unresolved chain link angles: 12 Unresolved chain link dihedrals: 9 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.86, per 1000 atoms: 0.20 Number of scatterers: 39693 At special positions: 0 Unit cell: (180.88, 192.85, 207.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 1158 15.00 O 10792 8.00 N 7140 7.00 C 20518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.0 seconds 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3530 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 29 sheets defined 25.6% alpha, 18.3% beta 331 base pairs and 574 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.622A pdb=" N PHE A 16 " --> pdb=" O ASN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 141 through 157 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'B' and resid 61 through 84 removed outlier: 3.648A pdb=" N ILE B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 163 Processing helix chain 'C' and resid 8 through 19 removed outlier: 4.006A pdb=" N PHE C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 15 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 42 removed outlier: 3.635A pdb=" N LYS C 41 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 49 removed outlier: 3.766A pdb=" N ILE C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 removed outlier: 3.707A pdb=" N LEU C 67 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C 68 " --> pdb=" O ARG C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 68' Processing helix chain 'C' and resid 99 through 104 removed outlier: 3.845A pdb=" N GLN C 104 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.694A pdb=" N LEU C 137 " --> pdb=" O GLN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 39 through 51 removed outlier: 3.691A pdb=" N LYS D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR D 50 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 removed outlier: 3.896A pdb=" N VAL D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 115 removed outlier: 3.519A pdb=" N CYS D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR D 115 " --> pdb=" O LYS D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 134 Processing helix chain 'E' and resid 118 through 125 Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'F' and resid 5 through 10 removed outlier: 3.704A pdb=" N ARG F 10 " --> pdb=" O ARG F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 74 Processing helix chain 'F' and resid 146 through 159 removed outlier: 3.551A pdb=" N TYR F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE F 159 " --> pdb=" O SER F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 188 removed outlier: 3.513A pdb=" N LYS F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 43 removed outlier: 3.521A pdb=" N GLU G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 59 Processing helix chain 'H' and resid 1 through 14 removed outlier: 3.626A pdb=" N LEU H 5 " --> pdb=" O ILE H 1 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR H 12 " --> pdb=" O LEU H 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 41 removed outlier: 3.500A pdb=" N LEU I 35 " --> pdb=" O SER I 31 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS I 36 " --> pdb=" O LYS I 32 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU I 39 " --> pdb=" O LEU I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 88 Processing helix chain 'I' and resid 122 through 134 Processing helix chain 'I' and resid 166 through 178 Processing helix chain 'I' and resid 192 through 196 removed outlier: 4.302A pdb=" N GLY I 196 " --> pdb=" O CYS I 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 192 through 196' Processing helix chain 'I' and resid 211 through 223 Processing helix chain 'J' and resid 34 through 42 Processing helix chain 'J' and resid 45 through 51 removed outlier: 4.000A pdb=" N GLU J 49 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL J 50 " --> pdb=" O ASP J 46 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 45 through 51' Processing helix chain 'J' and resid 67 through 76 Processing helix chain 'J' and resid 79 through 91 Processing helix chain 'J' and resid 96 through 116 removed outlier: 3.820A pdb=" N PHE J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 141 removed outlier: 3.649A pdb=" N ILE J 133 " --> pdb=" O THR J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 165 Processing helix chain 'J' and resid 182 through 194 removed outlier: 4.453A pdb=" N LEU J 186 " --> pdb=" O GLU J 182 " (cutoff:3.500A) Proline residue: J 192 - end of helix Processing helix chain 'J' and resid 217 through 230 removed outlier: 3.628A pdb=" N LYS J 225 " --> pdb=" O ASP J 221 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS J 226 " --> pdb=" O GLU J 222 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU J 227 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR J 228 " --> pdb=" O ILE J 224 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 277 through 283 removed outlier: 5.700A pdb=" N VAL A 279 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLY A 222 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARG A 281 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 220 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL A 223 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA A 343 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N HIS A 55 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILE A 367 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 57 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 277 through 283 removed outlier: 5.700A pdb=" N VAL A 279 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLY A 222 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARG A 281 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 220 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL A 223 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA A 343 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS A 50 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLU A 80 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 52 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 364 through 367 removed outlier: 6.525A pdb=" N VAL A 57 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILE A 367 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N HIS A 55 " --> pdb=" O ILE A 367 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 101 through 106 removed outlier: 3.512A pdb=" N LYS A 103 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'A' and resid 181 through 185 removed outlier: 6.831A pdb=" N ARG A 162 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU A 89 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE A 164 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL A 87 " --> pdb=" O TRP A 106 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TRP A 106 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 89 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR A 104 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY A 91 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 181 through 185 removed outlier: 6.831A pdb=" N ARG A 162 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU A 89 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE A 164 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.508A pdb=" N GLY A 228 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 8 through 11 Processing sheet with id=BB, first strand: chain 'B' and resid 17 through 20 Processing sheet with id=BC, first strand: chain 'B' and resid 131 through 133 removed outlier: 3.685A pdb=" N VAL B 143 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS B 89 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing sheet with id=BD, first strand: chain 'B' and resid 101 through 104 removed outlier: 3.826A pdb=" N VAL B 110 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 50 through 52 removed outlier: 6.979A pdb=" N MET C 26 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE C 191 " --> pdb=" O MET C 26 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL C 28 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 187 " --> pdb=" O GLU C 30 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 106 through 107 removed outlier: 3.617A pdb=" N TYR C 184 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 145 through 146 Processing sheet with id=DA, first strand: chain 'D' and resid 15 through 16 removed outlier: 4.187A pdb=" N ARG D 16 " --> pdb=" O LYS D 61 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS D 61 " --> pdb=" O ARG D 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=DA Processing sheet with id=EA, first strand: chain 'E' and resid 17 through 18 Processing sheet with id=EB, first strand: chain 'E' and resid 22 through 24 removed outlier: 5.237A pdb=" N VAL E 36 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR E 61 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA E 99 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=EC, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=FA, first strand: chain 'F' and resid 133 through 140 removed outlier: 6.444A pdb=" N ILE F 134 " --> pdb=" O SER F 54 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N SER F 54 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 166 " --> pdb=" O HIS F 51 " (cutoff:3.500A) Processing sheet with id=FB, first strand: chain 'F' and resid 59 through 61 removed outlier: 6.135A pdb=" N ILE F 99 " --> pdb=" O PRO F 122 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY F 124 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing sheet with id=GA, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=IA, first strand: chain 'I' and resid 2 through 4 removed outlier: 3.522A pdb=" N VAL I 198 " --> pdb=" O ILE I 205 " (cutoff:3.500A) Processing sheet with id=IB, first strand: chain 'I' and resid 17 through 19 Processing sheet with id=IC, first strand: chain 'I' and resid 64 through 65 removed outlier: 3.566A pdb=" N ALA I 64 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU I 72 " --> pdb=" O GLN I 95 " (cutoff:3.500A) Processing sheet with id=ID, first strand: chain 'I' and resid 109 through 110 removed outlier: 3.516A pdb=" N ALA I 109 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing sheet with id=IE, first strand: chain 'I' and resid 152 through 154 removed outlier: 3.549A pdb=" N ALA I 153 " --> pdb=" O LEU I 160 " (cutoff:3.500A) Processing sheet with id=JA, first strand: chain 'J' and resid 26 through 31 removed outlier: 3.838A pdb=" N VAL J 17 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing sheet with id=JB, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.746A pdb=" N GLN J 64 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id=JC, first strand: chain 'J' and resid 195 through 200 removed outlier: 6.298A pdb=" N VAL J 196 " --> pdb=" O ILE J 212 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE J 212 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU J 198 " --> pdb=" O CYS J 210 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS J 210 " --> pdb=" O GLU J 198 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL J 209 " --> pdb=" O PHE J 176 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU J 174 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N HIS J 171 " --> pdb=" O LYS J 240 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS J 240 " --> pdb=" O HIS J 171 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG J 173 " --> pdb=" O ASN J 238 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE J 177 " --> pdb=" O LEU J 234 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU J 234 " --> pdb=" O ILE J 177 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 804 hydrogen bonds 1350 hydrogen bond angles 0 basepair planarities 331 basepair parallelities 574 stacking parallelities Total time for adding SS restraints: 16.35 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4421 1.32 - 1.45: 17831 1.45 - 1.57: 18180 1.57 - 1.69: 2310 1.69 - 1.81: 129 Bond restraints: 42871 Sorted by residual: bond pdb=" O3' C N3131 " pdb=" P A N3132 " ideal model delta sigma weight residual 1.607 1.558 0.049 1.20e-02 6.94e+03 1.66e+01 bond pdb=" O3' A N3146 " pdb=" P G N3147 " ideal model delta sigma weight residual 1.607 1.562 0.045 1.20e-02 6.94e+03 1.41e+01 bond pdb=" O3' G N3421 " pdb=" P C N3422 " ideal model delta sigma weight residual 1.607 1.562 0.045 1.20e-02 6.94e+03 1.40e+01 bond pdb=" O3' G N2666 " pdb=" P A N2667 " ideal model delta sigma weight residual 1.607 1.564 0.043 1.20e-02 6.94e+03 1.27e+01 bond pdb=" N HIS A 321 " pdb=" CA HIS A 321 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.16e+01 ... (remaining 42866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 60254 3.03 - 6.06: 3122 6.06 - 9.09: 155 9.09 - 12.12: 14 12.12 - 15.15: 3 Bond angle restraints: 63548 Sorted by residual: angle pdb=" O3' G N2995 " pdb=" C3' G N2995 " pdb=" C2' G N2995 " ideal model delta sigma weight residual 113.80 128.95 -15.15 2.00e+00 2.50e-01 5.74e+01 angle pdb=" N PRO D 88 " pdb=" CA PRO D 88 " pdb=" C PRO D 88 " ideal model delta sigma weight residual 110.70 119.36 -8.66 1.22e+00 6.72e-01 5.04e+01 angle pdb=" C4' G N1565 " pdb=" C3' G N1565 " pdb=" O3' G N1565 " ideal model delta sigma weight residual 112.50 125.88 -13.38 2.00e+00 2.50e-01 4.47e+01 angle pdb=" O3' A N1582 " pdb=" C3' A N1582 " pdb=" C2' A N1582 " ideal model delta sigma weight residual 113.80 126.41 -12.61 2.00e+00 2.50e-01 3.97e+01 angle pdb=" N ARG A 269 " pdb=" CA ARG A 269 " pdb=" C ARG A 269 " ideal model delta sigma weight residual 108.32 118.59 -10.27 1.64e+00 3.72e-01 3.92e+01 ... (remaining 63543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 20951 35.45 - 70.89: 2204 70.89 - 106.34: 145 106.34 - 141.78: 4 141.78 - 177.23: 8 Dihedral angle restraints: 23312 sinusoidal: 17837 harmonic: 5475 Sorted by residual: dihedral pdb=" C4' G N1368 " pdb=" C3' G N1368 " pdb=" C2' G N1368 " pdb=" C1' G N1368 " ideal model delta sinusoidal sigma weight residual 36.34 -44.79 81.13 1 3.10e+00 1.04e-01 8.45e+02 dihedral pdb=" C4' A N1594 " pdb=" C3' A N1594 " pdb=" C2' A N1594 " pdb=" C1' A N1594 " ideal model delta sinusoidal sigma weight residual 36.34 -43.38 79.72 1 3.10e+00 1.04e-01 8.21e+02 dihedral pdb=" C4' G N3047 " pdb=" C3' G N3047 " pdb=" C2' G N3047 " pdb=" C1' G N3047 " ideal model delta sinusoidal sigma weight residual 36.34 -41.55 77.90 1 3.10e+00 1.04e-01 7.89e+02 ... (remaining 23309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 5164 0.121 - 0.243: 2483 0.243 - 0.364: 463 0.364 - 0.486: 11 0.486 - 0.607: 2 Chirality restraints: 8123 Sorted by residual: chirality pdb=" C3' G N1565 " pdb=" C4' G N1565 " pdb=" O3' G N1565 " pdb=" C2' G N1565 " both_signs ideal model delta sigma weight residual False -2.50 -1.89 -0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" C3' G N1457 " pdb=" C4' G N1457 " pdb=" O3' G N1457 " pdb=" C2' G N1457 " both_signs ideal model delta sigma weight residual False -2.50 -1.96 -0.54 2.00e-01 2.50e+01 7.25e+00 chirality pdb=" C3' G N2995 " pdb=" C4' G N2995 " pdb=" O3' G N2995 " pdb=" C2' G N2995 " both_signs ideal model delta sigma weight residual False -2.50 -2.03 -0.47 2.00e-01 2.50e+01 5.60e+00 ... (remaining 8120 not shown) Planarity restraints: 3754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C N1393 " 0.025 2.00e-02 2.50e+03 4.70e-02 4.97e+01 pdb=" N1 C N1393 " -0.028 2.00e-02 2.50e+03 pdb=" C2 C N1393 " -0.023 2.00e-02 2.50e+03 pdb=" O2 C N1393 " 0.064 2.00e-02 2.50e+03 pdb=" N3 C N1393 " -0.103 2.00e-02 2.50e+03 pdb=" C4 C N1393 " 0.012 2.00e-02 2.50e+03 pdb=" N4 C N1393 " 0.054 2.00e-02 2.50e+03 pdb=" C5 C N1393 " 0.005 2.00e-02 2.50e+03 pdb=" C6 C N1393 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G N1385 " 0.003 2.00e-02 2.50e+03 3.65e-02 3.99e+01 pdb=" N9 G N1385 " -0.019 2.00e-02 2.50e+03 pdb=" C8 G N1385 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G N1385 " 0.011 2.00e-02 2.50e+03 pdb=" C5 G N1385 " 0.009 2.00e-02 2.50e+03 pdb=" C6 G N1385 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G N1385 " -0.063 2.00e-02 2.50e+03 pdb=" N1 G N1385 " 0.095 2.00e-02 2.50e+03 pdb=" C2 G N1385 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G N1385 " -0.048 2.00e-02 2.50e+03 pdb=" N3 G N1385 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G N1385 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C N3462 " 0.031 2.00e-02 2.50e+03 4.08e-02 3.75e+01 pdb=" N1 C N3462 " -0.018 2.00e-02 2.50e+03 pdb=" C2 C N3462 " 0.013 2.00e-02 2.50e+03 pdb=" O2 C N3462 " -0.066 2.00e-02 2.50e+03 pdb=" N3 C N3462 " 0.091 2.00e-02 2.50e+03 pdb=" C4 C N3462 " -0.006 2.00e-02 2.50e+03 pdb=" N4 C N3462 " -0.024 2.00e-02 2.50e+03 pdb=" C5 C N3462 " -0.013 2.00e-02 2.50e+03 pdb=" C6 C N3462 " -0.009 2.00e-02 2.50e+03 ... (remaining 3751 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 3 1.93 - 2.67: 1954 2.67 - 3.42: 50654 3.42 - 4.16: 126798 4.16 - 4.90: 175671 Nonbonded interactions: 355080 Sorted by model distance: nonbonded pdb=" N1 A N2425 " pdb=" O4 U N2442 " model vdw 1.192 2.496 nonbonded pdb=" O4 U N2676 " pdb=" N1 A N3134 " model vdw 1.537 2.496 nonbonded pdb=" C2 A N2425 " pdb=" O4 U N2442 " model vdw 1.931 3.340 nonbonded pdb=" O6 G N1541 " pdb=" O2' A N2632 " model vdw 2.142 3.040 nonbonded pdb=" O TYR A 134 " pdb=" OH TYR A 138 " model vdw 2.181 3.040 ... (remaining 355075 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.160 Set scattering table: 0.170 Process input model: 45.880 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 42871 Z= 0.433 Angle : 1.361 15.155 63548 Z= 0.695 Chirality : 0.134 0.607 8123 Planarity : 0.007 0.140 3754 Dihedral : 21.273 177.229 19782 Min Nonbonded Distance : 1.192 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 2.86 % Allowed : 9.12 % Favored : 88.01 % Rotamer: Outliers : 2.32 % Allowed : 6.54 % Favored : 91.13 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 1.47 % Twisted General : 0.16 % 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: -3.68 (0.15), residues: 1885 helix: -0.93 (0.21), residues: 430 sheet: -2.89 (0.26), residues: 271 loop : -3.10 (0.14), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 48 TYR 0.028 0.003 TYR A 134 PHE 0.024 0.003 PHE B 115 TRP 0.021 0.002 TRP A 258 HIS 0.012 0.002 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.43 (42871) covalent geometry : angle 1.36102 / 0.69 (63548) hydrogen bonds : bond 0.15880 / 10.69 ( 1214) hydrogen bonds : angle 9.87535 / 6.98 ( 2553) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 441 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5400 (mtt) cc_final: 0.5089 (mtt) REVERT: A 61 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6753 (tp30) REVERT: A 71 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7779 (mt-10) REVERT: A 79 ILE cc_start: 0.9086 (pt) cc_final: 0.8681 (mt) REVERT: A 99 LEU cc_start: 0.7343 (mp) cc_final: 0.6930 (mp) REVERT: A 100 LYS cc_start: 0.5734 (tptp) cc_final: 0.5125 (mmmt) REVERT: A 156 LYS cc_start: 0.7971 (ttpp) cc_final: 0.7756 (ttmt) REVERT: A 171 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7824 (mmtm) REVERT: A 178 LYS cc_start: 0.6427 (OUTLIER) cc_final: 0.6204 (mppt) REVERT: A 193 GLU cc_start: 0.7958 (tt0) cc_final: 0.7724 (tt0) REVERT: A 224 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8489 (p) REVERT: A 261 SER cc_start: 0.7701 (m) cc_final: 0.7098 (p) REVERT: A 262 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6695 (mtm-85) REVERT: A 273 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8711 (tt) REVERT: A 282 ASN cc_start: 0.8586 (m-40) cc_final: 0.8300 (m110) REVERT: A 347 ARG cc_start: 0.7990 (mtt90) cc_final: 0.5956 (ttp-170) REVERT: A 348 LYS cc_start: 0.8486 (mttt) cc_final: 0.8191 (mttt) REVERT: A 366 PHE cc_start: 0.7241 (m-80) cc_final: 0.7014 (m-80) REVERT: B 20 VAL cc_start: 0.8716 (p) cc_final: 0.8410 (t) REVERT: B 21 LYS cc_start: 0.7652 (tttp) cc_final: 0.6768 (tppt) REVERT: B 26 LYS cc_start: 0.8164 (mttm) cc_final: 0.7589 (ttmm) REVERT: B 34 LEU cc_start: 0.8233 (mt) cc_final: 0.8006 (mt) REVERT: B 52 GLU cc_start: 0.7749 (mt-10) cc_final: 0.6631 (mm-30) REVERT: B 70 THR cc_start: 0.8265 (m) cc_final: 0.7942 (p) REVERT: B 109 VAL cc_start: 0.8420 (p) cc_final: 0.7615 (m) REVERT: B 125 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6764 (mm-30) REVERT: B 167 TYR cc_start: 0.6935 (m-80) cc_final: 0.6427 (m-80) REVERT: C 25 LYS cc_start: 0.3914 (mmtt) cc_final: 0.3491 (mmmt) REVERT: C 56 LYS cc_start: 0.1393 (mptt) cc_final: 0.0960 (mtmm) REVERT: D 25 MET cc_start: 0.1007 (mtt) cc_final: 0.0670 (ttp) REVERT: D 99 LYS cc_start: 0.4708 (pttm) cc_final: 0.4351 (pttm) REVERT: D 116 MET cc_start: 0.1968 (ttm) cc_final: 0.1606 (tpt) REVERT: E 33 ASN cc_start: 0.8390 (m110) cc_final: 0.8081 (m-40) REVERT: E 51 SER cc_start: 0.9071 (m) cc_final: 0.8785 (m) REVERT: E 83 LYS cc_start: 0.8715 (tptp) cc_final: 0.6110 (mptt) REVERT: E 106 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7322 (mmtt) REVERT: E 112 ASN cc_start: 0.7325 (p0) cc_final: 0.6928 (p0) REVERT: E 125 TRP cc_start: 0.8470 (m100) cc_final: 0.8251 (m100) REVERT: E 127 LYS cc_start: 0.7965 (tptm) cc_final: 0.7738 (tppt) REVERT: F 22 TYR cc_start: 0.8551 (m-80) cc_final: 0.8330 (m-80) REVERT: F 78 LYS cc_start: 0.6066 (mttt) cc_final: 0.5850 (mptt) REVERT: F 123 MET cc_start: 0.7171 (ttt) cc_final: 0.6952 (ttt) REVERT: F 143 ASN cc_start: 0.7299 (m110) cc_final: 0.7086 (m-40) REVERT: F 144 MET cc_start: 0.7226 (mtt) cc_final: 0.6973 (mtm) REVERT: F 153 ARG cc_start: 0.7915 (ttt90) cc_final: 0.7545 (ttt-90) REVERT: G 50 ARG cc_start: 0.5850 (ptm-80) cc_final: 0.3257 (mtt90) REVERT: H 17 MET cc_start: 0.7938 (mmt) cc_final: 0.7246 (mmt) REVERT: I 1 MET cc_start: 0.3776 (mmm) cc_final: 0.2179 (tmm) REVERT: I 24 CYS cc_start: 0.6645 (t) cc_final: 0.6378 (t) REVERT: I 62 LEU cc_start: 0.5396 (tp) cc_final: 0.5130 (tt) REVERT: I 80 GLU cc_start: 0.5773 (mt-10) cc_final: 0.5541 (mt-10) REVERT: I 86 ASN cc_start: 0.6255 (m-40) cc_final: 0.6048 (m-40) REVERT: I 111 ASN cc_start: 0.7391 (p0) cc_final: 0.6794 (p0) REVERT: I 136 GLU cc_start: 0.4001 (tt0) cc_final: 0.3739 (tp30) REVERT: I 155 THR cc_start: 0.6098 (p) cc_final: 0.5885 (p) REVERT: I 164 MET cc_start: 0.5094 (mmt) cc_final: 0.4681 (mtm) REVERT: J 21 LYS cc_start: 0.6838 (tttp) cc_final: 0.6557 (ttpt) REVERT: J 35 LYS cc_start: 0.4610 (mttm) cc_final: 0.4247 (mtmm) REVERT: J 145 LYS cc_start: 0.6652 (mmtm) cc_final: 0.6108 (ttmt) REVERT: J 188 GLU cc_start: 0.6285 (mm-30) cc_final: 0.5943 (tt0) REVERT: J 200 GLU cc_start: 0.3202 (mt-10) cc_final: 0.2789 (mt-10) REVERT: J 209 VAL cc_start: 0.3732 (m) cc_final: 0.3342 (p) outliers start: 38 outliers final: 13 residues processed: 470 average time/residue: 0.2988 time to fit residues: 216.2146 Evaluate side-chains 335 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 317 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain J residue 128 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 HIS ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN A 166 HIS A 168 GLN A 276 HIS ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS B 40 HIS B 46 ASN B 114 ASN B 135 ASN B 147 ASN C 93 ASN C 164 GLN D 103 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 177 ASN G 30 HIS H 43 ASN I 40 ASN J 14 ASN J 121 ASN J 147 ASN J 181 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.187831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.165288 restraints weight = 55855.426| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 0.60 r_work: 0.3470 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 42871 Z= 0.367 Angle : 1.511 19.670 63548 Z= 0.617 Chirality : 0.133 1.501 8123 Planarity : 0.006 0.151 3754 Dihedral : 18.812 179.913 16037 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.65 % Favored : 90.66 % Rotamer: Outliers : 4.16 % Allowed : 13.33 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.17), residues: 1885 helix: 0.15 (0.25), residues: 448 sheet: -2.22 (0.28), residues: 267 loop : -2.87 (0.15), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 342 TYR 0.025 0.003 TYR B 133 PHE 0.018 0.002 PHE B 115 TRP 0.020 0.003 TRP A 122 HIS 0.013 0.002 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00748 / 0.37 (42871) covalent geometry : angle 1.51111 / 0.62 (63548) hydrogen bonds : bond 0.07586 / 4.76 ( 1214) hydrogen bonds : angle 5.12892 / 3.65 ( 2553) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 319 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6106 (mtt) cc_final: 0.5557 (mtt) REVERT: A 61 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6861 (tp30) REVERT: A 68 HIS cc_start: 0.6404 (OUTLIER) cc_final: 0.5939 (m90) REVERT: A 100 LYS cc_start: 0.5640 (tptp) cc_final: 0.5248 (mmmt) REVERT: A 132 THR cc_start: 0.6652 (m) cc_final: 0.6375 (m) REVERT: A 171 LYS cc_start: 0.8520 (mmtm) cc_final: 0.8317 (mmtm) REVERT: A 178 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6800 (mptp) REVERT: A 261 SER cc_start: 0.7663 (m) cc_final: 0.7249 (p) REVERT: A 347 ARG cc_start: 0.8200 (mtt90) cc_final: 0.6716 (ttp-170) REVERT: A 348 LYS cc_start: 0.8768 (mttt) cc_final: 0.8567 (mttp) REVERT: A 388 PHE cc_start: 0.5722 (m-10) cc_final: 0.5484 (m-80) REVERT: A 395 SER cc_start: 0.4902 (OUTLIER) cc_final: 0.3996 (m) REVERT: B 21 LYS cc_start: 0.7642 (tttp) cc_final: 0.7333 (tmtt) REVERT: B 26 LYS cc_start: 0.8339 (mttm) cc_final: 0.7794 (tttt) REVERT: B 52 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7075 (mm-30) REVERT: B 75 ILE cc_start: 0.8647 (pt) cc_final: 0.8313 (mt) REVERT: B 82 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8588 (t) REVERT: B 167 TYR cc_start: 0.6782 (m-80) cc_final: 0.6065 (m-80) REVERT: C 56 LYS cc_start: 0.1012 (mptt) cc_final: 0.0436 (mtmm) REVERT: C 98 LYS cc_start: 0.3058 (mttt) cc_final: 0.2153 (mmtm) REVERT: D 25 MET cc_start: 0.1169 (mtt) cc_final: 0.0869 (ttp) REVERT: D 56 MET cc_start: 0.3215 (mtt) cc_final: 0.2284 (mmt) REVERT: D 99 LYS cc_start: 0.5932 (pttm) cc_final: 0.4622 (pttp) REVERT: D 116 MET cc_start: 0.2029 (ttm) cc_final: 0.1828 (tpt) REVERT: E 1 MET cc_start: 0.7105 (tpp) cc_final: 0.6723 (tpt) REVERT: E 51 SER cc_start: 0.9014 (m) cc_final: 0.8810 (m) REVERT: E 106 LYS cc_start: 0.8442 (mtmt) cc_final: 0.8098 (ptpp) REVERT: E 112 ASN cc_start: 0.7398 (p0) cc_final: 0.7150 (p0) REVERT: E 125 TRP cc_start: 0.8530 (m100) cc_final: 0.8327 (m100) REVERT: F 1 MET cc_start: 0.5659 (tpt) cc_final: 0.5446 (tpt) REVERT: F 24 ARG cc_start: 0.6177 (OUTLIER) cc_final: 0.5741 (pmm150) REVERT: F 59 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8222 (mt0) REVERT: F 144 MET cc_start: 0.7228 (mtt) cc_final: 0.7010 (mtm) REVERT: G 50 ARG cc_start: 0.6307 (ptm-80) cc_final: 0.4096 (mtt90) REVERT: H 17 MET cc_start: 0.7671 (mmt) cc_final: 0.7406 (mmt) REVERT: H 44 LEU cc_start: 0.8514 (mm) cc_final: 0.8298 (mm) REVERT: I 1 MET cc_start: 0.4662 (mmm) cc_final: 0.2555 (tmm) REVERT: I 8 GLU cc_start: 0.5303 (mt-10) cc_final: 0.5070 (mt-10) REVERT: I 50 GLU cc_start: 0.4919 (mt-10) cc_final: 0.4342 (mt-10) REVERT: I 62 LEU cc_start: 0.6259 (tp) cc_final: 0.5733 (tt) REVERT: I 111 ASN cc_start: 0.6958 (p0) cc_final: 0.6524 (p0) REVERT: J 35 LYS cc_start: 0.4940 (mttm) cc_final: 0.4579 (mtmm) REVERT: J 201 ASP cc_start: 0.6704 (t0) cc_final: 0.6421 (t0) outliers start: 68 outliers final: 40 residues processed: 365 average time/residue: 0.2709 time to fit residues: 157.3675 Evaluate side-chains 314 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 267 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 83 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 chunk 260 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 74 optimal weight: 40.0000 chunk 205 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN A 68 HIS A 170 HIS A 176 GLN A 180 HIS ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS A 277 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN C 133 GLN E 33 ASN E 98 ASN F 112 GLN I 86 ASN I 118 HIS J 80 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.188991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.172277 restraints weight = 55870.117| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 0.90 r_work: 0.3445 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 42871 Z= 0.322 Angle : 1.292 17.000 63548 Z= 0.528 Chirality : 0.106 1.154 8123 Planarity : 0.006 0.151 3754 Dihedral : 19.178 179.891 16025 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.02 % Favored : 90.40 % Rotamer: Outliers : 5.75 % Allowed : 15.05 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.17), residues: 1885 helix: 0.20 (0.25), residues: 433 sheet: -2.13 (0.28), residues: 261 loop : -2.74 (0.15), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 58 TYR 0.028 0.003 TYR B 133 PHE 0.016 0.002 PHE B 115 TRP 0.020 0.003 TRP F 171 HIS 0.008 0.002 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.32 (42871) covalent geometry : angle 1.29218 / 0.53 (63548) hydrogen bonds : bond 0.07715 / 4.91 ( 1214) hydrogen bonds : angle 4.80556 / 3.43 ( 2553) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 296 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5669 (mtt) cc_final: 0.5277 (mtt) REVERT: A 13 ASN cc_start: 0.8640 (t0) cc_final: 0.8164 (t0) REVERT: A 61 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6750 (tp30) REVERT: A 67 MET cc_start: 0.4161 (OUTLIER) cc_final: 0.3933 (mmm) REVERT: A 89 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8804 (tp) REVERT: A 92 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.6615 (t80) REVERT: A 100 LYS cc_start: 0.5721 (tptp) cc_final: 0.5349 (mmmt) REVERT: A 117 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.5238 (mtt-85) REVERT: A 178 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6890 (mptp) REVERT: A 347 ARG cc_start: 0.8001 (mtt90) cc_final: 0.6627 (ttp-170) REVERT: A 395 SER cc_start: 0.4733 (OUTLIER) cc_final: 0.3855 (m) REVERT: B 21 LYS cc_start: 0.7488 (tttp) cc_final: 0.7239 (tmtt) REVERT: B 26 LYS cc_start: 0.8022 (mttm) cc_final: 0.7510 (tttt) REVERT: B 35 SER cc_start: 0.7797 (m) cc_final: 0.7572 (p) REVERT: B 48 VAL cc_start: 0.7602 (OUTLIER) cc_final: 0.7311 (t) REVERT: B 75 ILE cc_start: 0.8534 (pt) cc_final: 0.8272 (mt) REVERT: B 91 ARG cc_start: 0.8090 (mtp180) cc_final: 0.7829 (mtp-110) REVERT: C 1 MET cc_start: 0.1046 (ptt) cc_final: -0.0526 (mmp) REVERT: D 25 MET cc_start: 0.2170 (mtt) cc_final: 0.1812 (ttp) REVERT: D 56 MET cc_start: 0.2579 (mtt) cc_final: 0.2166 (mmt) REVERT: D 99 LYS cc_start: 0.5908 (pttm) cc_final: 0.4710 (pptt) REVERT: E 1 MET cc_start: 0.6843 (tpp) cc_final: 0.6303 (tpp) REVERT: E 51 SER cc_start: 0.9050 (m) cc_final: 0.8759 (m) REVERT: E 112 ASN cc_start: 0.7087 (p0) cc_final: 0.6595 (p0) REVERT: F 144 MET cc_start: 0.7237 (mtt) cc_final: 0.6992 (mtm) REVERT: F 153 ARG cc_start: 0.8903 (ttt-90) cc_final: 0.8676 (ttt-90) REVERT: G 50 ARG cc_start: 0.7000 (ptm-80) cc_final: 0.4793 (mtt90) REVERT: I 1 MET cc_start: 0.4394 (mmm) cc_final: 0.2505 (tmm) REVERT: I 50 GLU cc_start: 0.5027 (mt-10) cc_final: 0.4725 (mt-10) REVERT: I 80 GLU cc_start: 0.6058 (mt-10) cc_final: 0.5778 (mt-10) REVERT: I 111 ASN cc_start: 0.7138 (p0) cc_final: 0.6782 (p0) REVERT: J 35 LYS cc_start: 0.4924 (mttm) cc_final: 0.4670 (mtpp) outliers start: 94 outliers final: 56 residues processed: 361 average time/residue: 0.2687 time to fit residues: 155.1236 Evaluate side-chains 323 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 259 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 194 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 260 optimal weight: 6.9990 chunk 289 optimal weight: 9.9990 chunk 270 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 222 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 271 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN A 277 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN E 33 ASN E 98 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN I 140 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.185943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.161973 restraints weight = 55858.527| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.59 r_work: 0.3366 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 42871 Z= 0.317 Angle : 1.275 15.556 63548 Z= 0.519 Chirality : 0.104 1.036 8123 Planarity : 0.006 0.152 3754 Dihedral : 19.081 179.738 16024 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.23 % Favored : 90.24 % Rotamer: Outliers : 5.14 % Allowed : 17.19 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.17), residues: 1885 helix: 0.08 (0.25), residues: 438 sheet: -1.86 (0.29), residues: 251 loop : -2.71 (0.15), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 58 TYR 0.025 0.002 TYR B 133 PHE 0.020 0.002 PHE B 115 TRP 0.016 0.002 TRP F 171 HIS 0.008 0.002 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.32 (42871) covalent geometry : angle 1.27527 / 0.52 (63548) hydrogen bonds : bond 0.07509 / 4.74 ( 1214) hydrogen bonds : angle 4.71065 / 3.37 ( 2553) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 265 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5352 (mtt) cc_final: 0.4938 (mtt) REVERT: A 13 ASN cc_start: 0.8642 (t0) cc_final: 0.8186 (t0) REVERT: A 61 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6572 (tp30) REVERT: A 89 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8836 (tp) REVERT: A 92 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.6243 (t80) REVERT: A 100 LYS cc_start: 0.5798 (tptp) cc_final: 0.5372 (mmmt) REVERT: A 117 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.5330 (mtt-85) REVERT: A 137 GLN cc_start: 0.4286 (OUTLIER) cc_final: 0.3612 (tm-30) REVERT: A 233 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8491 (mm) REVERT: A 272 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: A 347 ARG cc_start: 0.8046 (mtt90) cc_final: 0.6550 (ttp80) REVERT: A 395 SER cc_start: 0.5123 (OUTLIER) cc_final: 0.4216 (m) REVERT: B 21 LYS cc_start: 0.7591 (tttp) cc_final: 0.7322 (tmtt) REVERT: B 26 LYS cc_start: 0.8060 (mttm) cc_final: 0.7623 (tttt) REVERT: B 48 VAL cc_start: 0.7671 (OUTLIER) cc_final: 0.7426 (t) REVERT: B 82 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8597 (t) REVERT: B 171 ARG cc_start: 0.8405 (mpp80) cc_final: 0.8141 (mtm-85) REVERT: C 1 MET cc_start: 0.0861 (ptt) cc_final: -0.0416 (mmm) REVERT: D 56 MET cc_start: 0.3415 (mtt) cc_final: 0.2514 (mmt) REVERT: D 99 LYS cc_start: 0.5729 (pttm) cc_final: 0.4501 (pptt) REVERT: E 1 MET cc_start: 0.6706 (tpp) cc_final: 0.6410 (tpt) REVERT: E 51 SER cc_start: 0.9110 (m) cc_final: 0.8821 (m) REVERT: E 112 ASN cc_start: 0.7179 (p0) cc_final: 0.6819 (p0) REVERT: E 125 TRP cc_start: 0.8536 (m100) cc_final: 0.8240 (m100) REVERT: F 21 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7729 (ptt-90) REVERT: F 24 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5605 (pmm150) REVERT: F 115 MET cc_start: 0.8328 (mtm) cc_final: 0.7884 (mtp) REVERT: G 50 ARG cc_start: 0.7217 (ptm-80) cc_final: 0.4749 (mtt180) REVERT: I 1 MET cc_start: 0.4549 (mmm) cc_final: 0.2658 (tmm) REVERT: I 50 GLU cc_start: 0.5321 (mt-10) cc_final: 0.5120 (mt-10) REVERT: I 80 GLU cc_start: 0.6054 (mt-10) cc_final: 0.5638 (mt-10) REVERT: I 111 ASN cc_start: 0.6866 (p0) cc_final: 0.6420 (p0) REVERT: I 118 HIS cc_start: 0.6032 (OUTLIER) cc_final: 0.5819 (t-90) REVERT: J 35 LYS cc_start: 0.4696 (mttm) cc_final: 0.4293 (mtpp) outliers start: 84 outliers final: 51 residues processed: 326 average time/residue: 0.2695 time to fit residues: 138.9921 Evaluate side-chains 318 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 254 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 118 HIS Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 194 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 70 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 253 optimal weight: 8.9990 chunk 210 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS B 154 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 98 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 HIS J 9 GLN J 101 HIS J 238 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.180972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.162291 restraints weight = 56092.437| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.11 r_work: 0.3321 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 42871 Z= 0.442 Angle : 1.442 17.163 63548 Z= 0.585 Chirality : 0.116 1.139 8123 Planarity : 0.007 0.152 3754 Dihedral : 19.352 179.826 16023 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.66 % Favored : 88.81 % Rotamer: Outliers : 6.91 % Allowed : 17.80 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % 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: -3.01 (0.17), residues: 1885 helix: -0.41 (0.24), residues: 451 sheet: -2.13 (0.28), residues: 252 loop : -2.78 (0.15), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 235 TYR 0.027 0.003 TYR A 286 PHE 0.036 0.003 PHE B 115 TRP 0.019 0.003 TRP F 171 HIS 0.012 0.002 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00908 / 0.44 (42871) covalent geometry : angle 1.44163 / 0.58 (63548) hydrogen bonds : bond 0.08620 / 5.41 ( 1214) hydrogen bonds : angle 4.84334 / 3.45 ( 2553) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 290 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ASN cc_start: 0.8514 (t0) cc_final: 0.8096 (t0) REVERT: A 68 HIS cc_start: 0.6420 (OUTLIER) cc_final: 0.6144 (m170) REVERT: A 89 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8886 (tp) REVERT: A 92 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.6138 (t80) REVERT: A 100 LYS cc_start: 0.5761 (tptp) cc_final: 0.3573 (mmtt) REVERT: A 117 ARG cc_start: 0.5957 (OUTLIER) cc_final: 0.5230 (mtt-85) REVERT: A 137 GLN cc_start: 0.4758 (OUTLIER) cc_final: 0.4555 (tm-30) REVERT: A 233 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8514 (mm) REVERT: A 272 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: A 341 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8149 (pttt) REVERT: A 347 ARG cc_start: 0.8169 (mtt90) cc_final: 0.6722 (ttp-170) REVERT: A 395 SER cc_start: 0.5004 (OUTLIER) cc_final: 0.4116 (m) REVERT: B 21 LYS cc_start: 0.7743 (tttp) cc_final: 0.7388 (tmtt) REVERT: B 26 LYS cc_start: 0.8149 (mttm) cc_final: 0.7779 (tttt) REVERT: B 48 VAL cc_start: 0.7581 (OUTLIER) cc_final: 0.7291 (t) REVERT: B 54 THR cc_start: 0.8372 (t) cc_final: 0.7850 (p) REVERT: B 120 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7501 (tp) REVERT: B 122 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7206 (mtt90) REVERT: B 171 ARG cc_start: 0.8474 (mpp80) cc_final: 0.7868 (mtm-85) REVERT: C 1 MET cc_start: 0.0467 (OUTLIER) cc_final: -0.0139 (mmt) REVERT: D 56 MET cc_start: 0.3142 (mtt) cc_final: 0.2263 (mmt) REVERT: D 99 LYS cc_start: 0.5410 (pttm) cc_final: 0.4035 (pptt) REVERT: E 1 MET cc_start: 0.7005 (tpp) cc_final: 0.6745 (tpt) REVERT: E 56 ASP cc_start: 0.8855 (m-30) cc_final: 0.8527 (m-30) REVERT: E 112 ASN cc_start: 0.7183 (p0) cc_final: 0.6653 (p0) REVERT: E 125 TRP cc_start: 0.8567 (m100) cc_final: 0.8209 (m100) REVERT: F 21 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7769 (ptt-90) REVERT: F 24 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5655 (pmm150) REVERT: F 147 ASN cc_start: 0.8283 (m-40) cc_final: 0.8008 (m110) REVERT: F 171 TRP cc_start: 0.7733 (m100) cc_final: 0.7345 (t-100) REVERT: I 1 MET cc_start: 0.4244 (mmm) cc_final: 0.3817 (mmp) REVERT: I 25 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7370 (mp) REVERT: I 32 LYS cc_start: 0.4511 (OUTLIER) cc_final: 0.2960 (mmmt) REVERT: I 111 ASN cc_start: 0.7059 (p0) cc_final: 0.6589 (p0) REVERT: J 5 THR cc_start: 0.6152 (p) cc_final: 0.5866 (p) REVERT: J 35 LYS cc_start: 0.4948 (mttm) cc_final: 0.4568 (mtpp) REVERT: J 68 LYS cc_start: 0.3976 (OUTLIER) cc_final: 0.2630 (ttmt) outliers start: 113 outliers final: 74 residues processed: 366 average time/residue: 0.2607 time to fit residues: 152.3719 Evaluate side-chains 363 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 272 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 75 TYR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain J residue 197 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 59 optimal weight: 30.0000 chunk 279 optimal weight: 5.9990 chunk 299 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 64 optimal weight: 30.0000 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS A 39 GLN A 215 ASN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 98 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN I 86 ASN J 238 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.189757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.169423 restraints weight = 55643.644| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 0.56 r_work: 0.3552 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 42871 Z= 0.228 Angle : 1.157 14.858 63548 Z= 0.470 Chirality : 0.093 0.952 8123 Planarity : 0.005 0.151 3754 Dihedral : 19.174 179.963 16020 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.01 % Favored : 91.46 % Rotamer: Outliers : 5.57 % Allowed : 20.49 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.17), residues: 1885 helix: 0.11 (0.25), residues: 444 sheet: -1.77 (0.29), residues: 241 loop : -2.61 (0.15), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 269 TYR 0.024 0.002 TYR A 286 PHE 0.020 0.002 PHE B 115 TRP 0.010 0.002 TRP F 171 HIS 0.007 0.001 HIS H 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.23 (42871) covalent geometry : angle 1.15651 / 0.47 (63548) hydrogen bonds : bond 0.07185 / 4.51 ( 1214) hydrogen bonds : angle 4.56578 / 3.26 ( 2553) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 284 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASN cc_start: 0.8408 (t0) cc_final: 0.7951 (t0) REVERT: A 89 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8786 (tp) REVERT: A 92 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.6123 (t80) REVERT: A 100 LYS cc_start: 0.5599 (tptp) cc_final: 0.5188 (mmmt) REVERT: A 117 ARG cc_start: 0.5869 (OUTLIER) cc_final: 0.5173 (mtt-85) REVERT: A 347 ARG cc_start: 0.7990 (mtt90) cc_final: 0.6767 (ttp-170) REVERT: A 361 LYS cc_start: 0.7691 (mppt) cc_final: 0.7474 (mppt) REVERT: A 395 SER cc_start: 0.4774 (OUTLIER) cc_final: 0.4068 (m) REVERT: B 20 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8063 (t) REVERT: B 21 LYS cc_start: 0.7453 (tttp) cc_final: 0.7145 (tppt) REVERT: B 26 LYS cc_start: 0.8046 (mttm) cc_final: 0.7648 (tttt) REVERT: B 48 VAL cc_start: 0.7408 (OUTLIER) cc_final: 0.7102 (t) REVERT: B 70 THR cc_start: 0.8418 (t) cc_final: 0.8210 (p) REVERT: B 91 ARG cc_start: 0.8078 (mtp180) cc_final: 0.7821 (mtp-110) REVERT: B 120 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7305 (tp) REVERT: B 171 ARG cc_start: 0.8477 (mpp80) cc_final: 0.8002 (mtm-85) REVERT: C 1 MET cc_start: 0.0434 (ptt) cc_final: -0.0111 (mmt) REVERT: D 56 MET cc_start: 0.3428 (mtt) cc_final: 0.2404 (mmt) REVERT: D 99 LYS cc_start: 0.5166 (pttm) cc_final: 0.3698 (pptt) REVERT: E 1 MET cc_start: 0.7029 (tpp) cc_final: 0.6811 (tpt) REVERT: E 51 SER cc_start: 0.9093 (m) cc_final: 0.8848 (m) REVERT: E 72 LYS cc_start: 0.7944 (ttmm) cc_final: 0.6825 (ttpt) REVERT: E 112 ASN cc_start: 0.7174 (p0) cc_final: 0.6642 (p0) REVERT: E 125 TRP cc_start: 0.8476 (m100) cc_final: 0.8071 (m100) REVERT: F 21 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7655 (ptt-90) REVERT: F 24 ARG cc_start: 0.6544 (OUTLIER) cc_final: 0.5737 (pmm150) REVERT: F 136 PHE cc_start: 0.7914 (m-80) cc_final: 0.7710 (m-80) REVERT: F 147 ASN cc_start: 0.8080 (m-40) cc_final: 0.7807 (m110) REVERT: H 15 ASP cc_start: 0.7311 (t0) cc_final: 0.7101 (t0) REVERT: H 34 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7038 (ptt90) REVERT: H 44 LEU cc_start: 0.8596 (mm) cc_final: 0.8323 (mm) REVERT: I 1 MET cc_start: 0.4553 (mmm) cc_final: 0.2762 (tmm) REVERT: J 35 LYS cc_start: 0.4888 (mttm) cc_final: 0.4548 (mtpp) REVERT: J 165 MET cc_start: 0.2741 (tpp) cc_final: 0.2450 (tpp) outliers start: 91 outliers final: 61 residues processed: 343 average time/residue: 0.2585 time to fit residues: 141.9378 Evaluate side-chains 340 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 269 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 75 TYR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 187 LYS Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain J residue 197 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 32 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 205 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN A 215 ASN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 98 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 ASN J 238 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.186755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.166894 restraints weight = 55637.988| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 0.55 r_work: 0.3488 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 42871 Z= 0.309 Angle : 1.246 14.555 63548 Z= 0.505 Chirality : 0.100 0.987 8123 Planarity : 0.006 0.153 3754 Dihedral : 19.161 179.417 16020 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.08 % Favored : 89.44 % Rotamer: Outliers : 6.61 % Allowed : 19.57 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.18), residues: 1885 helix: 0.02 (0.25), residues: 441 sheet: -2.03 (0.28), residues: 255 loop : -2.56 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 342 TYR 0.023 0.002 TYR A 286 PHE 0.022 0.002 PHE B 115 TRP 0.013 0.002 TRP F 171 HIS 0.008 0.002 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.31 (42871) covalent geometry : angle 1.24563 / 0.51 (63548) hydrogen bonds : bond 0.07561 / 4.70 ( 1214) hydrogen bonds : angle 4.60286 / 3.27 ( 2553) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 270 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ASN cc_start: 0.8458 (t0) cc_final: 0.8006 (t0) REVERT: A 35 ASP cc_start: 0.5291 (t0) cc_final: 0.5035 (t0) REVERT: A 89 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8841 (tp) REVERT: A 92 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.6016 (t80) REVERT: A 100 LYS cc_start: 0.5693 (tptp) cc_final: 0.5286 (mmmt) REVERT: A 117 ARG cc_start: 0.5726 (OUTLIER) cc_final: 0.4901 (mtt-85) REVERT: A 233 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8466 (mm) REVERT: A 276 HIS cc_start: 0.5448 (OUTLIER) cc_final: 0.3856 (p90) REVERT: A 341 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7718 (pttt) REVERT: A 347 ARG cc_start: 0.7979 (mtt90) cc_final: 0.6606 (ttp-170) REVERT: A 395 SER cc_start: 0.4670 (OUTLIER) cc_final: 0.3836 (m) REVERT: B 21 LYS cc_start: 0.7460 (tttp) cc_final: 0.7253 (tppt) REVERT: B 26 LYS cc_start: 0.8068 (mttm) cc_final: 0.7635 (tttt) REVERT: B 48 VAL cc_start: 0.7434 (OUTLIER) cc_final: 0.7129 (t) REVERT: B 82 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8560 (t) REVERT: B 120 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7422 (tp) REVERT: B 171 ARG cc_start: 0.8523 (mpp80) cc_final: 0.8011 (mtm-85) REVERT: C 1 MET cc_start: 0.0552 (OUTLIER) cc_final: 0.0078 (mmt) REVERT: D 56 MET cc_start: 0.3326 (mtt) cc_final: 0.2066 (mmt) REVERT: D 99 LYS cc_start: 0.5197 (pttm) cc_final: 0.3639 (pptt) REVERT: E 1 MET cc_start: 0.7112 (tpp) cc_final: 0.6864 (tpt) REVERT: E 32 LYS cc_start: 0.8533 (mmtt) cc_final: 0.8255 (mttm) REVERT: E 72 LYS cc_start: 0.8000 (ttmm) cc_final: 0.6840 (ttpt) REVERT: E 112 ASN cc_start: 0.7143 (p0) cc_final: 0.6624 (p0) REVERT: E 125 TRP cc_start: 0.8408 (m100) cc_final: 0.8016 (m100) REVERT: F 21 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7712 (ptt-90) REVERT: F 24 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.5806 (pmm150) REVERT: F 33 ILE cc_start: 0.8192 (mp) cc_final: 0.7826 (mm) REVERT: F 147 ASN cc_start: 0.8244 (m-40) cc_final: 0.7965 (m110) REVERT: H 15 ASP cc_start: 0.7248 (t0) cc_final: 0.7020 (t0) REVERT: H 34 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7087 (ptt90) REVERT: I 1 MET cc_start: 0.4292 (mmm) cc_final: 0.3459 (mmp) REVERT: I 32 LYS cc_start: 0.4758 (OUTLIER) cc_final: 0.3257 (mmmt) REVERT: I 111 ASN cc_start: 0.6758 (p0) cc_final: 0.6272 (p0) REVERT: J 5 THR cc_start: 0.5872 (p) cc_final: 0.5558 (p) REVERT: J 35 LYS cc_start: 0.4860 (mttm) cc_final: 0.4535 (mtpp) REVERT: J 68 LYS cc_start: 0.3683 (OUTLIER) cc_final: 0.2489 (ttmt) outliers start: 108 outliers final: 77 residues processed: 346 average time/residue: 0.2532 time to fit residues: 139.4722 Evaluate side-chains 350 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 257 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 72 CYS Chi-restraints excluded: chain F residue 75 TYR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 187 LYS Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 220 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 292 optimal weight: 5.9990 chunk 253 optimal weight: 8.9990 chunk 237 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 290 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 121 optimal weight: 40.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 98 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN J 238 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.189224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.169938 restraints weight = 55374.765| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 0.52 r_work: 0.3543 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 42871 Z= 0.245 Angle : 1.163 13.596 63548 Z= 0.473 Chirality : 0.094 0.928 8123 Planarity : 0.005 0.153 3754 Dihedral : 19.162 179.860 16020 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.44 % Favored : 91.09 % Rotamer: Outliers : 5.75 % Allowed : 20.67 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.18), residues: 1885 helix: 0.18 (0.25), residues: 440 sheet: -1.91 (0.29), residues: 252 loop : -2.46 (0.16), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 269 TYR 0.020 0.002 TYR B 133 PHE 0.021 0.002 PHE B 115 TRP 0.010 0.002 TRP F 171 HIS 0.007 0.001 HIS H 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.24 (42871) covalent geometry : angle 1.16266 / 0.47 (63548) hydrogen bonds : bond 0.07176 / 4.48 ( 1214) hydrogen bonds : angle 4.51277 / 3.21 ( 2553) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 258 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASN cc_start: 0.8411 (t0) cc_final: 0.7971 (t0) REVERT: A 35 ASP cc_start: 0.5264 (t0) cc_final: 0.4952 (t0) REVERT: A 89 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8802 (tp) REVERT: A 92 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.6237 (t80) REVERT: A 100 LYS cc_start: 0.5689 (tptp) cc_final: 0.5269 (mmmt) REVERT: A 117 ARG cc_start: 0.5796 (OUTLIER) cc_final: 0.5057 (mtt-85) REVERT: A 341 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7713 (pttt) REVERT: A 347 ARG cc_start: 0.7973 (mtt90) cc_final: 0.6649 (ttp-170) REVERT: A 395 SER cc_start: 0.4530 (OUTLIER) cc_final: 0.3804 (m) REVERT: B 1 MET cc_start: 0.6069 (OUTLIER) cc_final: 0.5821 (mtt) REVERT: B 21 LYS cc_start: 0.7531 (tttp) cc_final: 0.7282 (tppt) REVERT: B 26 LYS cc_start: 0.8021 (mttm) cc_final: 0.7637 (tttt) REVERT: B 48 VAL cc_start: 0.7437 (OUTLIER) cc_final: 0.7116 (t) REVERT: B 120 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7267 (tp) REVERT: C 1 MET cc_start: 0.0627 (OUTLIER) cc_final: 0.0200 (mmt) REVERT: D 56 MET cc_start: 0.3349 (mtt) cc_final: 0.2140 (mmt) REVERT: D 99 LYS cc_start: 0.5151 (pttm) cc_final: 0.3566 (pptt) REVERT: E 1 MET cc_start: 0.7026 (tpp) cc_final: 0.6685 (tpp) REVERT: E 72 LYS cc_start: 0.7807 (ttmm) cc_final: 0.6698 (ttpt) REVERT: E 112 ASN cc_start: 0.7087 (p0) cc_final: 0.6555 (p0) REVERT: E 125 TRP cc_start: 0.8404 (m100) cc_final: 0.8046 (m100) REVERT: F 21 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7630 (ptt-90) REVERT: F 24 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.5644 (pmm150) REVERT: F 33 ILE cc_start: 0.8104 (mp) cc_final: 0.7824 (mm) REVERT: F 147 ASN cc_start: 0.8235 (m-40) cc_final: 0.8000 (m110) REVERT: G 53 MET cc_start: 0.9039 (tpt) cc_final: 0.8455 (tpt) REVERT: H 15 ASP cc_start: 0.7296 (t0) cc_final: 0.7062 (t0) REVERT: H 34 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7181 (ptt90) REVERT: I 1 MET cc_start: 0.4417 (mmm) cc_final: 0.3665 (mmp) REVERT: I 111 ASN cc_start: 0.6808 (p0) cc_final: 0.6359 (p0) REVERT: J 35 LYS cc_start: 0.4867 (mttm) cc_final: 0.4537 (mtpp) REVERT: J 189 LYS cc_start: 0.7029 (mmtm) cc_final: 0.6813 (mmtt) outliers start: 94 outliers final: 73 residues processed: 319 average time/residue: 0.2723 time to fit residues: 138.1034 Evaluate side-chains 341 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 256 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 72 CYS Chi-restraints excluded: chain F residue 75 TYR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 187 LYS Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 220 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 185 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 chunk 128 optimal weight: 1.9990 chunk 158 optimal weight: 0.0980 chunk 298 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.187301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.167926 restraints weight = 55572.352| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 0.53 r_work: 0.3523 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 42871 Z= 0.294 Angle : 1.217 13.802 63548 Z= 0.494 Chirality : 0.098 0.961 8123 Planarity : 0.006 0.154 3754 Dihedral : 19.169 179.849 16020 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.66 % Favored : 89.87 % Rotamer: Outliers : 5.81 % Allowed : 20.49 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.18), residues: 1885 helix: 0.02 (0.25), residues: 446 sheet: -1.94 (0.29), residues: 257 loop : -2.49 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 269 TYR 0.021 0.002 TYR B 133 PHE 0.017 0.002 PHE J 57 TRP 0.013 0.002 TRP F 171 HIS 0.007 0.002 HIS H 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.29 (42871) covalent geometry : angle 1.21694 / 0.49 (63548) hydrogen bonds : bond 0.07446 / 4.62 ( 1214) hydrogen bonds : angle 4.55817 / 3.24 ( 2553) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 259 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ASN cc_start: 0.8431 (t0) cc_final: 0.7986 (t0) REVERT: A 35 ASP cc_start: 0.5598 (t0) cc_final: 0.5349 (t0) REVERT: A 67 MET cc_start: 0.2979 (mmm) cc_final: 0.2221 (mmm) REVERT: A 89 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8800 (tp) REVERT: A 92 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.5715 (t80) REVERT: A 100 LYS cc_start: 0.5714 (tptp) cc_final: 0.5324 (mmmt) REVERT: A 117 ARG cc_start: 0.5781 (OUTLIER) cc_final: 0.5029 (mtt-85) REVERT: A 233 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8487 (mm) REVERT: A 276 HIS cc_start: 0.5296 (OUTLIER) cc_final: 0.3665 (p90) REVERT: A 341 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7758 (pttt) REVERT: A 347 ARG cc_start: 0.7972 (mtt90) cc_final: 0.6675 (ttp-170) REVERT: A 395 SER cc_start: 0.4721 (OUTLIER) cc_final: 0.3938 (m) REVERT: B 21 LYS cc_start: 0.7631 (tttp) cc_final: 0.7334 (tppt) REVERT: B 26 LYS cc_start: 0.8060 (mttm) cc_final: 0.7637 (tttt) REVERT: B 48 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7185 (t) REVERT: C 1 MET cc_start: 0.0666 (OUTLIER) cc_final: 0.0305 (mmm) REVERT: D 56 MET cc_start: 0.3405 (mtt) cc_final: 0.2115 (mmt) REVERT: D 99 LYS cc_start: 0.4655 (pttm) cc_final: 0.3362 (pptt) REVERT: E 1 MET cc_start: 0.7047 (tpp) cc_final: 0.6712 (tpp) REVERT: E 72 LYS cc_start: 0.7881 (ttmm) cc_final: 0.6760 (ttpt) REVERT: E 112 ASN cc_start: 0.7105 (p0) cc_final: 0.6580 (p0) REVERT: E 125 TRP cc_start: 0.8466 (m100) cc_final: 0.8082 (m100) REVERT: F 21 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7708 (ptt-90) REVERT: F 24 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.5779 (pmm150) REVERT: F 33 ILE cc_start: 0.8112 (mp) cc_final: 0.7796 (mm) REVERT: F 38 ARG cc_start: 0.7668 (ptm-80) cc_final: 0.7003 (ptm-80) REVERT: F 196 ASN cc_start: 0.6419 (m110) cc_final: 0.6176 (m110) REVERT: I 1 MET cc_start: 0.4359 (mmm) cc_final: 0.3568 (mmp) REVERT: I 32 LYS cc_start: 0.4800 (OUTLIER) cc_final: 0.3320 (mmmt) REVERT: I 111 ASN cc_start: 0.6620 (p0) cc_final: 0.6167 (p0) REVERT: J 35 LYS cc_start: 0.4777 (mttm) cc_final: 0.4289 (mttm) REVERT: J 68 LYS cc_start: 0.3954 (OUTLIER) cc_final: 0.2777 (ttmt) outliers start: 95 outliers final: 74 residues processed: 321 average time/residue: 0.2799 time to fit residues: 143.4783 Evaluate side-chains 339 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 252 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 72 CYS Chi-restraints excluded: chain F residue 75 TYR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 187 LYS Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 232 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 296 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.187335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.166772 restraints weight = 55314.984| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 0.55 r_work: 0.3502 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 42871 Z= 0.280 Angle : 1.199 13.656 63548 Z= 0.488 Chirality : 0.096 0.951 8123 Planarity : 0.005 0.154 3754 Dihedral : 19.173 179.672 16020 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.97 % Favored : 90.56 % Rotamer: Outliers : 5.57 % Allowed : 20.67 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.18), residues: 1885 helix: -0.09 (0.25), residues: 457 sheet: -1.87 (0.29), residues: 255 loop : -2.47 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 269 TYR 0.021 0.002 TYR B 133 PHE 0.017 0.002 PHE J 57 TRP 0.011 0.002 TRP F 171 HIS 0.007 0.001 HIS H 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.28 (42871) covalent geometry : angle 1.19914 / 0.49 (63548) hydrogen bonds : bond 0.07357 / 4.57 ( 1214) hydrogen bonds : angle 4.54753 / 3.23 ( 2553) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 253 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.8432 (t0) cc_final: 0.7988 (t0) REVERT: A 35 ASP cc_start: 0.5611 (t0) cc_final: 0.5354 (t0) REVERT: A 89 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8794 (tp) REVERT: A 92 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.5636 (t80) REVERT: A 100 LYS cc_start: 0.5654 (tptp) cc_final: 0.5278 (mmmt) REVERT: A 117 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.5279 (mtt-85) REVERT: A 276 HIS cc_start: 0.5303 (OUTLIER) cc_final: 0.3648 (p90) REVERT: A 341 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7761 (pttt) REVERT: A 347 ARG cc_start: 0.7985 (mtt90) cc_final: 0.6684 (ttp-170) REVERT: A 395 SER cc_start: 0.4794 (OUTLIER) cc_final: 0.4037 (m) REVERT: B 1 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.6054 (mtt) REVERT: B 21 LYS cc_start: 0.7662 (tttp) cc_final: 0.7337 (tppt) REVERT: B 26 LYS cc_start: 0.8036 (mttm) cc_final: 0.7654 (tttt) REVERT: B 171 ARG cc_start: 0.8538 (mpp80) cc_final: 0.8037 (mtm-85) REVERT: C 1 MET cc_start: 0.0694 (OUTLIER) cc_final: 0.0327 (mmm) REVERT: D 56 MET cc_start: 0.3193 (mtt) cc_final: 0.2004 (mmt) REVERT: D 99 LYS cc_start: 0.4676 (pttm) cc_final: 0.3376 (pptt) REVERT: E 1 MET cc_start: 0.7016 (tpp) cc_final: 0.6699 (tpp) REVERT: E 72 LYS cc_start: 0.7896 (ttmm) cc_final: 0.6769 (ttpt) REVERT: E 112 ASN cc_start: 0.7136 (p0) cc_final: 0.6597 (p0) REVERT: E 125 TRP cc_start: 0.8471 (m100) cc_final: 0.8081 (m100) REVERT: F 21 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7676 (ptt-90) REVERT: F 24 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.5779 (pmm150) REVERT: F 33 ILE cc_start: 0.8092 (mp) cc_final: 0.7777 (mm) REVERT: F 38 ARG cc_start: 0.7666 (ptm-80) cc_final: 0.6961 (ptm-80) REVERT: F 196 ASN cc_start: 0.6379 (m110) cc_final: 0.6134 (m110) REVERT: H 34 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7147 (ptt90) REVERT: I 1 MET cc_start: 0.4321 (mmm) cc_final: 0.3539 (mmp) REVERT: I 17 LEU cc_start: 0.7123 (tt) cc_final: 0.6814 (tp) REVERT: I 32 LYS cc_start: 0.4889 (OUTLIER) cc_final: 0.3349 (mmmt) REVERT: I 111 ASN cc_start: 0.6516 (p0) cc_final: 0.5878 (p0) REVERT: J 1 MET cc_start: 0.2497 (ptp) cc_final: 0.0883 (mmm) REVERT: J 5 THR cc_start: 0.5894 (p) cc_final: 0.5585 (p) REVERT: J 35 LYS cc_start: 0.4834 (mttm) cc_final: 0.4354 (mttm) REVERT: J 68 LYS cc_start: 0.4131 (OUTLIER) cc_final: 0.2900 (ttmt) REVERT: J 165 MET cc_start: 0.3011 (tpp) cc_final: 0.2267 (ttt) REVERT: J 189 LYS cc_start: 0.6597 (mmtt) cc_final: 0.6129 (mmmt) outliers start: 91 outliers final: 73 residues processed: 313 average time/residue: 0.2845 time to fit residues: 141.1112 Evaluate side-chains 336 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 250 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 72 CYS Chi-restraints excluded: chain F residue 75 TYR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 30 HIS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 32 LYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 187 LYS Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 216 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 chunk 187 optimal weight: 30.0000 chunk 56 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN E 98 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.188173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.169127 restraints weight = 55729.442| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 0.53 r_work: 0.3542 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 42871 Z= 0.266 Angle : 1.183 13.701 63548 Z= 0.482 Chirality : 0.095 0.941 8123 Planarity : 0.005 0.154 3754 Dihedral : 19.165 179.732 16020 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.39 % Favored : 90.08 % Rotamer: Outliers : 5.38 % Allowed : 20.92 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 1.47 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.18), residues: 1885 helix: 0.02 (0.25), residues: 450 sheet: -1.80 (0.29), residues: 251 loop : -2.44 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 269 TYR 0.020 0.002 TYR B 133 PHE 0.017 0.002 PHE J 57 TRP 0.011 0.002 TRP F 171 HIS 0.007 0.001 HIS H 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.27 (42871) covalent geometry : angle 1.18334 / 0.48 (63548) hydrogen bonds : bond 0.07285 / 4.53 ( 1214) hydrogen bonds : angle 4.51824 / 3.21 ( 2553) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9868.83 seconds wall clock time: 170 minutes 0.17 seconds (10200.17 seconds total)