Starting phenix.real_space_refine on Fri Aug 7 08:51:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k28_36831/08_2026/8k28_36831.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k28_36831/08_2026/8k28_36831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k28_36831/08_2026/8k28_36831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k28_36831/08_2026/8k28_36831.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k28_36831/08_2026/8k28_36831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k28_36831/08_2026/8k28_36831.map" } resolution = 3.54 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= 0.007 sd= 0.083 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 119 5.49 5 S 70 5.16 5 C 12674 2.51 5 N 3523 2.21 5 O 4354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20740 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1345 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 165} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1898 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 234} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 6 Chain: "C" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2291 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2289 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2297 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2297 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 293} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2285 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 293} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1291 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 162} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 677 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "R" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 556 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "P" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1237 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 20, 'rna3p_pur': 13, 'rna3p_pyr': 15} Link IDs: {'rna2p': 31, 'rna3p': 27} Chain: "H" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2277 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 293} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'TRP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 33 Time building chain proxies: 5.04, per 1000 atoms: 0.24 Number of scatterers: 20740 At special positions: 0 Unit cell: (116.6, 138.6, 183.7, 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 70 16.00 P 119 15.00 O 4354 8.00 N 3523 7.00 C 12674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 764.6 milliseconds 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 47 sheets defined 25.4% alpha, 23.1% beta 29 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.685A pdb=" N ALA A 52 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 68 removed outlier: 4.003A pdb=" N VAL A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.673A pdb=" N ILE A 75 " --> pdb=" O MET A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 90 removed outlier: 4.008A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.787A pdb=" N ILE A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.915A pdb=" N ASN A 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS A 152 " --> pdb=" O PRO A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 152' Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.776A pdb=" N MET A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 42 removed outlier: 3.730A pdb=" N PHE B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY B 36 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 122 removed outlier: 4.312A pdb=" N LEU B 113 " --> pdb=" O CYS B 109 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.678A pdb=" N SER B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.586A pdb=" N ASP B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.898A pdb=" N LEU C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 126 " --> pdb=" O ASN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 179 removed outlier: 3.776A pdb=" N ALA C 167 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU C 168 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 235 Processing helix chain 'C' and resid 269 through 279 removed outlier: 3.774A pdb=" N ASP C 275 " --> pdb=" O PHE C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 298 Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.522A pdb=" N LEU D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 178 Processing helix chain 'D' and resid 225 through 234 removed outlier: 4.018A pdb=" N ARG D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 280 removed outlier: 3.552A pdb=" N ASP D 275 " --> pdb=" O PHE D 271 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY D 276 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'E' and resid 53 through 58 removed outlier: 4.173A pdb=" N ASP E 58 " --> pdb=" O ASN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.749A pdb=" N ASN E 122 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE E 123 " --> pdb=" O TYR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 178 removed outlier: 4.079A pdb=" N ILE E 169 " --> pdb=" O ASP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 Processing helix chain 'E' and resid 269 through 280 removed outlier: 3.818A pdb=" N LEU E 273 " --> pdb=" O ASP E 269 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP E 275 " --> pdb=" O PHE E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 298 Processing helix chain 'F' and resid 99 through 107 Processing helix chain 'F' and resid 112 through 125 removed outlier: 3.606A pdb=" N TYR F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE F 123 " --> pdb=" O TYR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 179 removed outlier: 3.954A pdb=" N ALA F 167 " --> pdb=" O ASP F 163 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N MET F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY F 179 " --> pdb=" O GLY F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 234 Processing helix chain 'F' and resid 269 through 280 removed outlier: 3.962A pdb=" N LEU F 273 " --> pdb=" O ASP F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 298 Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 99 through 107 Processing helix chain 'G' and resid 111 through 125 removed outlier: 3.677A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 179 removed outlier: 3.760A pdb=" N ILE G 169 " --> pdb=" O ASP G 165 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 234 removed outlier: 3.547A pdb=" N ALA G 232 " --> pdb=" O LYS G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 280 removed outlier: 3.745A pdb=" N LEU G 273 " --> pdb=" O ASP G 269 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP G 275 " --> pdb=" O PHE G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 296 removed outlier: 3.758A pdb=" N GLN G 288 " --> pdb=" O THR G 284 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE G 290 " --> pdb=" O GLU G 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 30 Processing helix chain 'I' and resid 62 through 69 removed outlier: 3.734A pdb=" N LEU I 66 " --> pdb=" O ASP I 62 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 109 removed outlier: 3.523A pdb=" N LEU I 102 " --> pdb=" O SER I 98 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG I 109 " --> pdb=" O ARG I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 121 removed outlier: 3.749A pdb=" N TYR I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 107 Processing helix chain 'H' and resid 111 through 125 removed outlier: 4.088A pdb=" N LEU H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE H 123 " --> pdb=" O TYR H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 177 removed outlier: 3.736A pdb=" N ILE H 169 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY H 175 " --> pdb=" O ASP H 171 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL H 176 " --> pdb=" O MET H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 234 removed outlier: 3.584A pdb=" N ALA H 232 " --> pdb=" O LYS H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 280 Processing helix chain 'H' and resid 284 through 298 removed outlier: 3.650A pdb=" N GLN H 288 " --> pdb=" O THR H 284 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET H 289 " --> pdb=" O GLU H 285 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG H 297 " --> pdb=" O ALA H 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.559A pdb=" N PHE A 17 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP A 45 " --> pdb=" O PHE A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 108 removed outlier: 3.836A pdb=" N GLY A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 108 removed outlier: 3.836A pdb=" N GLY A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ALA B 205 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LYS B 191 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU B 207 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N THR B 213 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL B 183 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 215 " --> pdb=" O PRO B 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.936A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ALA B 94 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY B 14 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU B 100 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYS B 8 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE B 102 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE B 6 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 104 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE B 4 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 59 removed outlier: 5.733A pdb=" N ALA B 94 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY B 14 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU B 100 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYS B 8 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE B 102 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE B 6 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 104 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE B 4 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 18 Processing sheet with id=AB2, first strand: chain 'C' and resid 16 through 18 removed outlier: 3.822A pdb=" N SER C 138 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 40 through 47 removed outlier: 3.560A pdb=" N GLY C 46 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N LEU C 211 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR C 64 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS C 213 " --> pdb=" O THR C 64 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 217 through 218 Processing sheet with id=AB5, first strand: chain 'C' and resid 254 through 255 removed outlier: 3.681A pdb=" N VAL C 255 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 260 " --> pdb=" O VAL C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.689A pdb=" N GLY D 299 " --> pdb=" O TYR D 12 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 16 through 18 Processing sheet with id=AB8, first strand: chain 'D' and resid 16 through 18 Processing sheet with id=AB9, first strand: chain 'D' and resid 40 through 44 removed outlier: 7.002A pdb=" N THR D 64 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS D 213 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 217 through 218 Processing sheet with id=AC2, first strand: chain 'D' and resid 254 through 255 removed outlier: 3.745A pdb=" N VAL D 255 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 260 " --> pdb=" O VAL D 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AC4, first strand: chain 'E' and resid 16 through 18 Processing sheet with id=AC5, first strand: chain 'E' and resid 16 through 18 Processing sheet with id=AC6, first strand: chain 'E' and resid 40 through 47 removed outlier: 3.812A pdb=" N ASN E 61 " --> pdb=" O GLY E 46 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA E 68 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 217 through 218 Processing sheet with id=AC8, first strand: chain 'E' and resid 235 through 237 Processing sheet with id=AC9, first strand: chain 'E' and resid 254 through 255 Processing sheet with id=AD1, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AD2, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AD3, first strand: chain 'F' and resid 40 through 45 Processing sheet with id=AD4, first strand: chain 'F' and resid 203 through 204 removed outlier: 4.233A pdb=" N GLN F 214 " --> pdb=" O GLU F 204 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 217 through 218 Processing sheet with id=AD6, first strand: chain 'F' and resid 235 through 237 Processing sheet with id=AD7, first strand: chain 'F' and resid 254 through 255 removed outlier: 3.635A pdb=" N VAL F 260 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AD9, first strand: chain 'G' and resid 16 through 18 Processing sheet with id=AE1, first strand: chain 'G' and resid 16 through 18 removed outlier: 3.953A pdb=" N VAL G 145 " --> pdb=" O GLN G 148 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 39 through 44 removed outlier: 4.541A pdb=" N ALA G 68 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 217 through 218 Processing sheet with id=AE4, first strand: chain 'G' and resid 235 through 237 Processing sheet with id=AE5, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AE6, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.267A pdb=" N PHE I 148 " --> pdb=" O VAL I 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE8, first strand: chain 'H' and resid 16 through 18 Processing sheet with id=AE9, first strand: chain 'H' and resid 16 through 18 removed outlier: 3.767A pdb=" N VAL H 145 " --> pdb=" O GLN H 148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 40 through 43 Processing sheet with id=AF2, first strand: chain 'H' and resid 235 through 237 655 hydrogen bonds defined for protein. 1788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3415 1.31 - 1.44: 6236 1.44 - 1.57: 11330 1.57 - 1.70: 238 1.70 - 1.83: 126 Bond restraints: 21345 Sorted by residual: bond pdb=" CA ALA E 125 " pdb=" C ALA E 125 " ideal model delta sigma weight residual 1.523 1.423 0.100 1.34e-02 5.57e+03 5.54e+01 bond pdb=" CA GLU D 93 " pdb=" C GLU D 93 " ideal model delta sigma weight residual 1.523 1.429 0.094 1.34e-02 5.57e+03 4.91e+01 bond pdb=" CA ALA D 6 " pdb=" C ALA D 6 " ideal model delta sigma weight residual 1.528 1.446 0.082 1.18e-02 7.18e+03 4.82e+01 bond pdb=" CA ALA E 92 " pdb=" C ALA E 92 " ideal model delta sigma weight residual 1.528 1.439 0.089 1.33e-02 5.65e+03 4.44e+01 bond pdb=" CA TYR D 99 " pdb=" C TYR D 99 " ideal model delta sigma weight residual 1.523 1.434 0.089 1.34e-02 5.57e+03 4.42e+01 ... (remaining 21340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 28913 3.56 - 7.12: 466 7.12 - 10.68: 92 10.68 - 14.23: 13 14.23 - 17.79: 6 Bond angle restraints: 29490 Sorted by residual: angle pdb=" N ALA F 57 " pdb=" CA ALA F 57 " pdb=" C ALA F 57 " ideal model delta sigma weight residual 114.56 96.77 17.79 1.27e+00 6.20e-01 1.96e+02 angle pdb=" N PHE F 112 " pdb=" CA PHE F 112 " pdb=" C PHE F 112 " ideal model delta sigma weight residual 112.59 95.87 16.72 1.22e+00 6.72e-01 1.88e+02 angle pdb=" N ASP F 58 " pdb=" CA ASP F 58 " pdb=" C ASP F 58 " ideal model delta sigma weight residual 111.14 98.83 12.31 1.08e+00 8.57e-01 1.30e+02 angle pdb=" N SER D 100 " pdb=" CA SER D 100 " pdb=" C SER D 100 " ideal model delta sigma weight residual 114.04 101.36 12.68 1.24e+00 6.50e-01 1.05e+02 angle pdb=" C ALA D 6 " pdb=" N PRO D 7 " pdb=" CA PRO D 7 " ideal model delta sigma weight residual 119.76 110.87 8.89 1.00e+00 1.00e+00 7.90e+01 ... (remaining 29485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 11665 35.29 - 70.59: 790 70.59 - 105.88: 55 105.88 - 141.17: 2 141.17 - 176.47: 5 Dihedral angle restraints: 12517 sinusoidal: 5672 harmonic: 6845 Sorted by residual: dihedral pdb=" O4' U P 34 " pdb=" C1' U P 34 " pdb=" N1 U P 34 " pdb=" C2 U P 34 " ideal model delta sinusoidal sigma weight residual 200.00 49.50 150.50 1 1.50e+01 4.44e-03 7.98e+01 dihedral pdb=" N PRO F 54 " pdb=" C PRO F 54 " pdb=" CA PRO F 54 " pdb=" CB PRO F 54 " ideal model delta harmonic sigma weight residual 115.10 131.79 -16.69 0 2.50e+00 1.60e-01 4.46e+01 dihedral pdb=" O4' U P 35 " pdb=" C1' U P 35 " pdb=" N1 U P 35 " pdb=" C2 U P 35 " ideal model delta sinusoidal sigma weight residual -160.00 -80.46 -79.54 1 1.50e+01 4.44e-03 3.49e+01 ... (remaining 12514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 3281 0.145 - 0.290: 140 0.290 - 0.435: 11 0.435 - 0.579: 5 0.579 - 0.724: 1 Chirality restraints: 3438 Sorted by residual: chirality pdb=" CA PRO F 54 " pdb=" N PRO F 54 " pdb=" C PRO F 54 " pdb=" CB PRO F 54 " both_signs ideal model delta sigma weight residual False 2.72 1.99 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C3' U P 34 " pdb=" C4' U P 34 " pdb=" O3' U P 34 " pdb=" C2' U P 34 " both_signs ideal model delta sigma weight residual False -2.48 -1.92 -0.56 2.00e-01 2.50e+01 7.72e+00 chirality pdb=" CG LEU D 270 " pdb=" CB LEU D 270 " pdb=" CD1 LEU D 270 " pdb=" CD2 LEU D 270 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 7.07e+00 ... (remaining 3435 not shown) Planarity restraints: 3410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 45 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.86e+01 pdb=" C ALA G 45 " -0.075 2.00e-02 2.50e+03 pdb=" O ALA G 45 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY G 46 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 124 " -0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C ALA E 124 " 0.073 2.00e-02 2.50e+03 pdb=" O ALA E 124 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA E 125 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR H 245 " 0.066 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO H 246 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO H 246 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO H 246 " 0.054 5.00e-02 4.00e+02 ... (remaining 3407 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1064 2.70 - 3.25: 19175 3.25 - 3.80: 36665 3.80 - 4.35: 45318 4.35 - 4.90: 73134 Nonbonded interactions: 175356 Sorted by model distance: nonbonded pdb=" N TYR D 99 " pdb=" N SER D 100 " model vdw 2.151 2.560 nonbonded pdb=" N ALA F 57 " pdb=" N ASP F 58 " model vdw 2.229 2.560 nonbonded pdb=" N VAL F 50 " pdb=" O VAL F 50 " model vdw 2.241 2.496 nonbonded pdb=" N PHE F 112 " pdb=" N GLY F 113 " model vdw 2.262 2.560 nonbonded pdb=" O GLY A 39 " pdb=" OG1 THR A 42 " model vdw 2.268 3.040 ... (remaining 175351 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 58 or (resid 59 and (name N or name \ CA or name C or name O or name CB )) or resid 60 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 107 or (r \ esid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 t \ hrough 129 or (resid 130 and (name N or name CA or name C or name O or name CB ) \ ) or resid 131 through 132 or (resid 133 and (name N or name CA or name C or nam \ e O or name CB )) or resid 134 through 203 or (resid 204 and (name N or name CA \ or name C or name O or name CB )) or resid 205 through 209 or (resid 210 and (na \ me N or name CA or name C or name O or name CB )) or resid 211 through 256 or (r \ esid 257 and (name N or name CA or name C or name O or name CB )) or resid 258 t \ hrough 266 or (resid 267 and (name N or name CA or name C or name O or name CB ) \ ) or resid 268 through 303)) selection = (chain 'D' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 58 or (resid 59 and (name N or name \ CA or name C or name O or name CB )) or resid 60 through 106 or (resid 107 throu \ gh 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ ough 129 or (resid 130 and (name N or name CA or name C or name O or name CB )) \ or resid 131 through 132 or (resid 133 and (name N or name CA or name C or name \ O or name CB )) or resid 134 through 203 or (resid 204 and (name N or name CA or \ name C or name O or name CB )) or resid 205 through 209 or (resid 210 and (name \ N or name CA or name C or name O or name CB )) or resid 211 through 256 or (res \ id 257 and (name N or name CA or name C or name O or name CB )) or resid 258 thr \ ough 303)) selection = (chain 'E' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 58 or (resid 59 and (name N or name \ CA or name C or name O or name CB )) or resid 60 through 106 or (resid 107 throu \ gh 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ ough 129 or (resid 130 and (name N or name CA or name C or name O or name CB )) \ or resid 131 through 132 or (resid 133 and (name N or name CA or name C or name \ O or name CB )) or resid 134 through 203 or (resid 204 and (name N or name CA or \ name C or name O or name CB )) or resid 205 through 209 or (resid 210 and (name \ N or name CA or name C or name O or name CB )) or resid 211 through 256 or (res \ id 257 and (name N or name CA or name C or name O or name CB )) or resid 258 thr \ ough 266 or (resid 267 and (name N or name CA or name C or name O or name CB )) \ or resid 268 through 303)) selection = (chain 'F' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 97 or (resid 98 and (name N or name \ CA or name C or name O or name CB )) or resid 99 through 106 or (resid 107 throu \ gh 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ ough 129 or (resid 130 and (name N or name CA or name C or name O or name CB )) \ or resid 131 through 132 or (resid 133 and (name N or name CA or name C or name \ O or name CB )) or resid 134 through 203 or (resid 204 and (name N or name CA or \ name C or name O or name CB )) or resid 205 through 209 or (resid 210 and (name \ N or name CA or name C or name O or name CB )) or resid 211 through 256 or (res \ id 257 and (name N or name CA or name C or name O or name CB )) or resid 258 thr \ ough 266 or (resid 267 and (name N or name CA or name C or name O or name CB )) \ or resid 268 through 303)) selection = (chain 'G' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 97 or (resid 98 and (name N or name \ CA or name C or name O or name CB )) or resid 99 through 106 or (resid 107 throu \ gh 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ ough 129 or (resid 130 and (name N or name CA or name C or name O or name CB )) \ or resid 131 through 132 or (resid 133 and (name N or name CA or name C or name \ O or name CB )) or resid 134 through 203 or (resid 204 and (name N or name CA or \ name C or name O or name CB )) or resid 205 through 256 or (resid 257 and (name \ N or name CA or name C or name O or name CB )) or resid 258 through 303)) selection = (chain 'H' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 58 or (resid 59 and (name N or name CA or name C \ or name O or name CB )) or resid 60 through 97 or (resid 98 and (name N or name \ CA or name C or name O or name CB )) or resid 99 through 106 or (resid 107 throu \ gh 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ ough 209 or (resid 210 and (name N or name CA or name C or name O or name CB )) \ or resid 211 through 266 or (resid 267 and (name N or name CA or name C or name \ O or name CB )) or resid 268 through 303)) } 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.190 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 21345 Z= 0.501 Angle : 1.200 17.793 29490 Z= 0.758 Chirality : 0.072 0.724 3438 Planarity : 0.007 0.100 3410 Dihedral : 21.076 176.466 8143 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.48 % Favored : 91.89 % Rotamer: Outliers : 4.20 % Allowed : 26.88 % Favored : 68.92 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.15), residues: 2379 helix: -2.68 (0.15), residues: 612 sheet: -0.75 (0.25), residues: 444 loop : -2.48 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 104 TYR 0.050 0.003 TYR D 81 PHE 0.054 0.003 PHE D 150 TRP 0.049 0.003 TRP H 28 HIS 0.021 0.002 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.50 (21345) covalent geometry : angle 1.20011 / 0.76 (29490) hydrogen bonds : bond 0.16943 / 11.21 ( 707) hydrogen bonds : angle 7.79720 / 5.43 ( 1930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 291 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 TYR cc_start: 0.7115 (m-10) cc_final: 0.6914 (m-80) REVERT: E 147 ASP cc_start: 0.6461 (m-30) cc_final: 0.5997 (t0) REVERT: F 267 LYS cc_start: 0.7546 (tttp) cc_final: 0.7336 (mtpp) REVERT: G 48 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: G 268 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7347 (p) REVERT: H 104 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7724 (pt0) REVERT: H 224 MET cc_start: 0.8152 (ptp) cc_final: 0.7714 (ptp) outliers start: 81 outliers final: 17 residues processed: 339 average time/residue: 0.1378 time to fit residues: 76.2379 Evaluate side-chains 242 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain H residue 278 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 50.0000 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 30.0000 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 ASN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 266 ASN ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 ASN ** H 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.154009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.111189 restraints weight = 47304.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.113552 restraints weight = 28074.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.114052 restraints weight = 18371.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.115220 restraints weight = 15498.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.115073 restraints weight = 13815.143| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21345 Z= 0.170 Angle : 0.676 9.971 29490 Z= 0.368 Chirality : 0.046 0.255 3438 Planarity : 0.005 0.067 3410 Dihedral : 20.823 176.003 4146 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.56 % Favored : 93.27 % Rotamer: Outliers : 4.77 % Allowed : 23.98 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.16), residues: 2379 helix: -1.55 (0.18), residues: 625 sheet: -0.79 (0.23), residues: 495 loop : -2.30 (0.15), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 104 TYR 0.030 0.002 TYR I 91 PHE 0.032 0.001 PHE A 9 TRP 0.015 0.001 TRP G 130 HIS 0.007 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (21345) covalent geometry : angle 0.67632 / 0.37 (29490) hydrogen bonds : bond 0.04756 / 3.15 ( 707) hydrogen bonds : angle 5.96422 / 4.13 ( 1930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 244 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 PHE cc_start: 0.6435 (t80) cc_final: 0.6105 (t80) REVERT: A 47 TYR cc_start: 0.6629 (t80) cc_final: 0.6408 (t80) REVERT: A 57 GLU cc_start: 0.7130 (mp0) cc_final: 0.6699 (tm-30) REVERT: B 158 CYS cc_start: 0.6157 (OUTLIER) cc_final: 0.5612 (m) REVERT: B 179 LEU cc_start: 0.6971 (tp) cc_final: 0.6761 (tt) REVERT: C 12 TYR cc_start: 0.7088 (m-10) cc_final: 0.6871 (m-10) REVERT: C 172 MET cc_start: 0.6163 (ptp) cc_final: 0.5430 (ptm) REVERT: C 234 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6284 (ttp-110) REVERT: C 295 LEU cc_start: 0.8849 (mp) cc_final: 0.8563 (tt) REVERT: E 143 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8090 (mm) REVERT: E 147 ASP cc_start: 0.6562 (m-30) cc_final: 0.6136 (t0) REVERT: F 228 LYS cc_start: 0.8456 (tttp) cc_final: 0.8064 (tttp) REVERT: G 48 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8003 (tp-100) REVERT: G 237 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7229 (m-30) REVERT: G 268 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7544 (p) REVERT: I 130 LYS cc_start: 0.7987 (pttm) cc_final: 0.7458 (pttp) outliers start: 92 outliers final: 54 residues processed: 316 average time/residue: 0.1302 time to fit residues: 68.4564 Evaluate side-chains 273 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 91 LYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 237 ASP Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 145 PHE Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 29 optimal weight: 0.0570 chunk 150 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN A 70 ASN B 74 GLN B 78 ASN D 82 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 61 ASN H 146 ASN H 148 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.150505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.107875 restraints weight = 47130.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.108489 restraints weight = 31002.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.109583 restraints weight = 20716.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.110333 restraints weight = 17036.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.110298 restraints weight = 14987.642| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 21345 Z= 0.225 Angle : 0.659 9.590 29490 Z= 0.359 Chirality : 0.046 0.358 3438 Planarity : 0.004 0.059 3410 Dihedral : 20.697 176.127 4139 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.27 % Favored : 92.64 % Rotamer: Outliers : 6.59 % Allowed : 22.37 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.16), residues: 2379 helix: -1.00 (0.20), residues: 619 sheet: -0.65 (0.24), residues: 479 loop : -2.13 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 127 TYR 0.036 0.002 TYR F 12 PHE 0.022 0.002 PHE I 145 TRP 0.011 0.002 TRP D 239 HIS 0.008 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (21345) covalent geometry : angle 0.65854 / 0.36 (29490) hydrogen bonds : bond 0.04460 / 2.95 ( 707) hydrogen bonds : angle 5.57165 / 3.84 ( 1930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 229 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.6693 (t80) cc_final: 0.6457 (t80) REVERT: A 57 GLU cc_start: 0.7195 (mp0) cc_final: 0.6682 (tm-30) REVERT: A 129 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8097 (mm-30) REVERT: A 165 GLN cc_start: 0.7259 (mp10) cc_final: 0.6874 (mp10) REVERT: B 226 PHE cc_start: 0.5829 (OUTLIER) cc_final: 0.5415 (m-80) REVERT: C 234 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6766 (ttp-110) REVERT: C 295 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8529 (mp) REVERT: D 88 ASP cc_start: 0.6332 (t0) cc_final: 0.6056 (t0) REVERT: E 143 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7972 (mt) REVERT: E 147 ASP cc_start: 0.6633 (m-30) cc_final: 0.6223 (t0) REVERT: E 273 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7105 (pp) REVERT: G 48 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: G 119 TYR cc_start: 0.8987 (m-80) cc_final: 0.8691 (m-80) REVERT: G 268 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7816 (p) REVERT: G 270 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7963 (tp) REVERT: I 3 ASN cc_start: 0.4517 (p0) cc_final: 0.4285 (p0) REVERT: I 121 TYR cc_start: 0.0578 (OUTLIER) cc_final: -0.0966 (t80) REVERT: I 130 LYS cc_start: 0.7919 (pttm) cc_final: 0.7549 (pttm) REVERT: H 104 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7838 (pt0) outliers start: 127 outliers final: 81 residues processed: 330 average time/residue: 0.1285 time to fit residues: 70.5090 Evaluate side-chains 301 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 211 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 91 LYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 121 TYR Chi-restraints excluded: chain I residue 145 PHE Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 148 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain H residue 296 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 28 optimal weight: 8.9990 chunk 21 optimal weight: 0.0970 chunk 198 optimal weight: 0.0170 chunk 225 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 0.0980 chunk 204 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.4420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN B 74 GLN B 78 ASN C 227 GLN D 61 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 HIS H 33 ASN H 148 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.153087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.110671 restraints weight = 47202.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.112462 restraints weight = 27443.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.113300 restraints weight = 17213.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.113953 restraints weight = 15643.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.114018 restraints weight = 13796.991| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21345 Z= 0.127 Angle : 0.603 10.200 29490 Z= 0.327 Chirality : 0.044 0.291 3438 Planarity : 0.004 0.054 3410 Dihedral : 20.631 177.323 4135 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.52 % Favored : 93.40 % Rotamer: Outliers : 5.86 % Allowed : 22.73 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.16), residues: 2379 helix: -0.76 (0.20), residues: 618 sheet: -0.58 (0.24), residues: 474 loop : -2.02 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 127 TYR 0.023 0.001 TYR F 12 PHE 0.022 0.001 PHE F 182 TRP 0.014 0.001 TRP D 130 HIS 0.006 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (21345) covalent geometry : angle 0.60260 / 0.33 (29490) hydrogen bonds : bond 0.03937 / 2.62 ( 707) hydrogen bonds : angle 5.32136 / 3.66 ( 1930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 237 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8079 (tpt170) cc_final: 0.7714 (tpt-90) REVERT: A 26 THR cc_start: 0.7399 (OUTLIER) cc_final: 0.6742 (m) REVERT: A 57 GLU cc_start: 0.7261 (mp0) cc_final: 0.6800 (tm-30) REVERT: A 58 GLU cc_start: 0.7878 (pm20) cc_final: 0.7300 (pm20) REVERT: A 70 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8109 (m-40) REVERT: A 83 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6525 (tp30) REVERT: A 165 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6781 (mp10) REVERT: B 84 ASN cc_start: 0.8410 (t0) cc_final: 0.8180 (m110) REVERT: B 226 PHE cc_start: 0.5858 (OUTLIER) cc_final: 0.5442 (m-80) REVERT: C 72 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.5959 (m90) REVERT: C 295 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8469 (mp) REVERT: D 56 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7206 (p0) REVERT: D 61 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7096 (p0) REVERT: E 133 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7990 (ttt-90) REVERT: E 143 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7896 (mt) REVERT: E 147 ASP cc_start: 0.6447 (m-30) cc_final: 0.6147 (t0) REVERT: E 180 GLU cc_start: 0.6100 (mm-30) cc_final: 0.5874 (mm-30) REVERT: E 273 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6998 (pp) REVERT: F 111 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7380 (t0) REVERT: G 48 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: G 119 TYR cc_start: 0.8982 (m-80) cc_final: 0.8712 (m-80) REVERT: G 185 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8299 (pp) REVERT: G 268 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7863 (p) REVERT: G 270 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8016 (tp) REVERT: I 121 TYR cc_start: 0.0567 (OUTLIER) cc_final: -0.0936 (t80) REVERT: I 130 LYS cc_start: 0.7982 (pttm) cc_final: 0.7620 (pttm) REVERT: H 104 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7847 (pt0) REVERT: H 274 MET cc_start: 0.8422 (ttm) cc_final: 0.8077 (ttm) outliers start: 113 outliers final: 68 residues processed: 322 average time/residue: 0.1323 time to fit residues: 70.4319 Evaluate side-chains 302 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 216 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 121 TYR Chi-restraints excluded: chain I residue 145 PHE Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 148 PHE Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 278 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 46 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 240 optimal weight: 9.9990 chunk 208 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 242 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 ASN ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN I 78 HIS H 61 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.150734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.107402 restraints weight = 46977.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.109305 restraints weight = 28078.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.110139 restraints weight = 17275.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.110734 restraints weight = 16200.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.110742 restraints weight = 14136.738| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21345 Z= 0.191 Angle : 0.638 10.138 29490 Z= 0.342 Chirality : 0.045 0.290 3438 Planarity : 0.004 0.054 3410 Dihedral : 20.509 176.818 4132 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.89 % Favored : 93.02 % Rotamer: Outliers : 6.33 % Allowed : 23.14 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.16), residues: 2379 helix: -0.70 (0.20), residues: 627 sheet: -0.56 (0.24), residues: 474 loop : -2.03 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 234 TYR 0.025 0.002 TYR F 12 PHE 0.021 0.002 PHE I 145 TRP 0.009 0.001 TRP E 239 HIS 0.008 0.001 HIS I 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (21345) covalent geometry : angle 0.63754 / 0.34 (29490) hydrogen bonds : bond 0.03946 / 2.60 ( 707) hydrogen bonds : angle 5.25120 / 3.60 ( 1930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 220 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.6348 (t80) cc_final: 0.5983 (t80) REVERT: A 57 GLU cc_start: 0.7330 (mp0) cc_final: 0.6797 (tm-30) REVERT: A 58 GLU cc_start: 0.7825 (pm20) cc_final: 0.7186 (pm20) REVERT: A 70 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8037 (t0) REVERT: A 165 GLN cc_start: 0.7489 (mp10) cc_final: 0.7268 (mp10) REVERT: B 226 PHE cc_start: 0.5858 (OUTLIER) cc_final: 0.5479 (m-80) REVERT: C 295 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8522 (mp) REVERT: D 56 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7074 (p0) REVERT: D 297 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8640 (ttp80) REVERT: E 133 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7990 (ttt-90) REVERT: E 143 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7975 (mt) REVERT: E 273 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7153 (pp) REVERT: F 111 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7422 (t0) REVERT: G 48 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: G 119 TYR cc_start: 0.8989 (m-80) cc_final: 0.8729 (m-80) REVERT: G 185 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8396 (pp) REVERT: G 268 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8095 (p) REVERT: G 270 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8033 (tp) REVERT: I 121 TYR cc_start: 0.0383 (OUTLIER) cc_final: -0.1189 (t80) REVERT: H 104 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7855 (pt0) outliers start: 122 outliers final: 86 residues processed: 316 average time/residue: 0.1310 time to fit residues: 68.8615 Evaluate side-chains 306 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 206 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 91 LYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 121 TYR Chi-restraints excluded: chain I residue 145 PHE Chi-restraints excluded: chain I residue 148 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 226 ASP Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 278 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 4 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN B 74 GLN C 72 HIS ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN E 82 ASN ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 HIS H 33 ASN H 61 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.151972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.109464 restraints weight = 46971.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.111167 restraints weight = 27689.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.112014 restraints weight = 17575.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.112411 restraints weight = 15590.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.112477 restraints weight = 14423.507| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21345 Z= 0.137 Angle : 0.606 10.217 29490 Z= 0.326 Chirality : 0.044 0.296 3438 Planarity : 0.004 0.071 3410 Dihedral : 20.453 177.362 4132 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.15 % Rotamer: Outliers : 5.97 % Allowed : 23.82 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.16), residues: 2379 helix: -0.63 (0.20), residues: 626 sheet: -0.47 (0.24), residues: 484 loop : -2.02 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 234 TYR 0.020 0.001 TYR D 12 PHE 0.022 0.001 PHE D 150 TRP 0.011 0.001 TRP E 239 HIS 0.007 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (21345) covalent geometry : angle 0.60563 / 0.33 (29490) hydrogen bonds : bond 0.03678 / 2.42 ( 707) hydrogen bonds : angle 5.14343 / 3.53 ( 1930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 224 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8138 (tpt-90) cc_final: 0.7815 (tpt-90) REVERT: A 26 THR cc_start: 0.7377 (OUTLIER) cc_final: 0.6945 (m) REVERT: A 47 TYR cc_start: 0.6490 (t80) cc_final: 0.6177 (t80) REVERT: A 57 GLU cc_start: 0.7348 (mp0) cc_final: 0.6827 (tm-30) REVERT: A 58 GLU cc_start: 0.7911 (pm20) cc_final: 0.7280 (pm20) REVERT: A 70 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8065 (m-40) REVERT: A 83 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6271 (tp30) REVERT: B 226 PHE cc_start: 0.5994 (OUTLIER) cc_final: 0.5606 (m-80) REVERT: C 12 TYR cc_start: 0.7290 (m-10) cc_final: 0.6869 (m-80) REVERT: C 295 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8419 (mp) REVERT: D 56 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7369 (p0) REVERT: E 133 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7941 (ttt-90) REVERT: E 143 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7881 (mt) REVERT: E 233 ILE cc_start: 0.9339 (mt) cc_final: 0.9093 (mt) REVERT: E 273 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7089 (pp) REVERT: F 111 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7257 (t0) REVERT: F 227 GLN cc_start: 0.8096 (pt0) cc_final: 0.7669 (pt0) REVERT: G 48 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: G 119 TYR cc_start: 0.8997 (m-80) cc_final: 0.8790 (m-80) REVERT: G 172 MET cc_start: 0.7571 (ppp) cc_final: 0.7288 (ppp) REVERT: G 185 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8274 (pp) REVERT: G 227 GLN cc_start: 0.8384 (pm20) cc_final: 0.8136 (pm20) REVERT: G 268 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8203 (p) REVERT: I 121 TYR cc_start: 0.0142 (OUTLIER) cc_final: -0.1352 (t80) REVERT: H 104 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7856 (pt0) outliers start: 115 outliers final: 83 residues processed: 311 average time/residue: 0.1246 time to fit residues: 64.7300 Evaluate side-chains 304 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 207 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 182 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 91 LYS Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 121 TYR Chi-restraints excluded: chain I residue 145 PHE Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 148 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 209 optimal weight: 50.0000 chunk 149 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 216 optimal weight: 50.0000 chunk 98 optimal weight: 0.9980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN B 74 GLN B 78 ASN C 72 HIS ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 ASN ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN H 33 ASN H 61 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.152778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.108825 restraints weight = 47151.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.111551 restraints weight = 25770.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.113512 restraints weight = 16393.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.113668 restraints weight = 15387.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.113724 restraints weight = 12565.243| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21345 Z= 0.186 Angle : 0.626 9.566 29490 Z= 0.335 Chirality : 0.044 0.294 3438 Planarity : 0.004 0.066 3410 Dihedral : 20.348 177.036 4128 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.15 % Favored : 92.77 % Rotamer: Outliers : 6.33 % Allowed : 24.08 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.16), residues: 2379 helix: -0.59 (0.21), residues: 625 sheet: -0.49 (0.24), residues: 484 loop : -2.02 (0.16), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 234 TYR 0.019 0.002 TYR A 47 PHE 0.023 0.001 PHE D 150 TRP 0.010 0.001 TRP E 239 HIS 0.005 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (21345) covalent geometry : angle 0.62599 / 0.33 (29490) hydrogen bonds : bond 0.03710 / 2.44 ( 707) hydrogen bonds : angle 5.18810 / 3.55 ( 1930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 218 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8204 (tpt-90) cc_final: 0.7859 (tpt-90) REVERT: A 26 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7175 (m) REVERT: A 47 TYR cc_start: 0.6508 (t80) cc_final: 0.6214 (t80) REVERT: A 57 GLU cc_start: 0.7308 (mp0) cc_final: 0.6768 (tm-30) REVERT: A 58 GLU cc_start: 0.7828 (pm20) cc_final: 0.7200 (pm20) REVERT: A 70 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8125 (m-40) REVERT: A 83 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6266 (tp30) REVERT: B 13 ASP cc_start: 0.7085 (m-30) cc_final: 0.6853 (t0) REVERT: B 226 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5664 (m-80) REVERT: C 12 TYR cc_start: 0.7236 (m-10) cc_final: 0.6916 (m-80) REVERT: C 295 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8414 (mp) REVERT: D 38 MET cc_start: 0.7912 (mmp) cc_final: 0.7667 (mmp) REVERT: D 56 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7332 (p0) REVERT: E 133 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7971 (ttt-90) REVERT: E 143 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.7864 (mt) REVERT: E 233 ILE cc_start: 0.9394 (mt) cc_final: 0.9147 (mt) REVERT: E 273 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7130 (pp) REVERT: F 111 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.7046 (t0) REVERT: F 227 GLN cc_start: 0.8276 (pt0) cc_final: 0.8012 (pt0) REVERT: F 294 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8548 (m-40) REVERT: G 48 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: G 172 MET cc_start: 0.7545 (ppp) cc_final: 0.7258 (ppp) REVERT: G 185 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8364 (pp) REVERT: G 268 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8340 (p) REVERT: I 121 TYR cc_start: 0.0254 (OUTLIER) cc_final: -0.1308 (t80) REVERT: H 104 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7864 (pt0) outliers start: 122 outliers final: 92 residues processed: 311 average time/residue: 0.1268 time to fit residues: 65.0969 Evaluate side-chains 314 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 207 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 294 ASN Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 91 LYS Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 239 TRP Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 121 TYR Chi-restraints excluded: chain I residue 145 PHE Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 148 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 300 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 50.0000 chunk 230 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 242 optimal weight: 0.0270 chunk 222 optimal weight: 0.0770 chunk 196 optimal weight: 30.0000 chunk 229 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 61 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.152513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.108720 restraints weight = 46736.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.110454 restraints weight = 28777.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.111261 restraints weight = 17913.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.111994 restraints weight = 16465.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111900 restraints weight = 14569.996| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21345 Z= 0.184 Angle : 0.624 9.231 29490 Z= 0.334 Chirality : 0.044 0.297 3438 Planarity : 0.004 0.064 3410 Dihedral : 20.323 177.110 4128 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.48 % Favored : 92.43 % Rotamer: Outliers : 6.54 % Allowed : 23.61 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.17), residues: 2379 helix: -0.54 (0.21), residues: 625 sheet: -0.45 (0.24), residues: 479 loop : -2.01 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 76 TYR 0.020 0.002 TYR D 12 PHE 0.026 0.001 PHE D 150 TRP 0.010 0.001 TRP E 239 HIS 0.005 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (21345) covalent geometry : angle 0.62430 / 0.33 (29490) hydrogen bonds : bond 0.03695 / 2.43 ( 707) hydrogen bonds : angle 5.18002 / 3.54 ( 1930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 215 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8230 (tpt-90) cc_final: 0.7883 (tpt-90) REVERT: A 26 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7240 (m) REVERT: A 47 TYR cc_start: 0.6533 (t80) cc_final: 0.6213 (t80) REVERT: A 57 GLU cc_start: 0.7319 (mp0) cc_final: 0.6783 (tm-30) REVERT: A 58 GLU cc_start: 0.7858 (pm20) cc_final: 0.7242 (pm20) REVERT: A 83 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6279 (tp30) REVERT: A 133 GLU cc_start: 0.6960 (pm20) cc_final: 0.6740 (pm20) REVERT: B 226 PHE cc_start: 0.6109 (OUTLIER) cc_final: 0.5730 (m-80) REVERT: C 12 TYR cc_start: 0.7196 (m-10) cc_final: 0.6916 (m-80) REVERT: C 295 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8409 (mp) REVERT: D 56 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7350 (p0) REVERT: E 133 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7997 (ttt-90) REVERT: E 143 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7938 (mt) REVERT: E 233 ILE cc_start: 0.9401 (mt) cc_final: 0.9168 (mt) REVERT: E 273 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7171 (pp) REVERT: F 111 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7070 (t0) REVERT: F 227 GLN cc_start: 0.8184 (pt0) cc_final: 0.7873 (pt0) REVERT: F 294 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8580 (m-40) REVERT: G 48 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: G 172 MET cc_start: 0.7609 (ppp) cc_final: 0.7312 (ppp) REVERT: G 185 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8375 (pp) REVERT: G 268 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8354 (p) REVERT: I 121 TYR cc_start: 0.0285 (OUTLIER) cc_final: -0.1324 (t80) REVERT: H 104 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7932 (pt0) REVERT: H 274 MET cc_start: 0.8391 (ttm) cc_final: 0.7955 (ttm) outliers start: 126 outliers final: 99 residues processed: 313 average time/residue: 0.1186 time to fit residues: 61.0960 Evaluate side-chains 320 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 207 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 182 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 294 ASN Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 91 LYS Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 239 TRP Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 121 TYR Chi-restraints excluded: chain I residue 145 PHE Chi-restraints excluded: chain I residue 148 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 219 ASN Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 3 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 210 optimal weight: 50.0000 chunk 113 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 78 ASN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 ASN ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN H 33 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.149679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.110614 restraints weight = 48778.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.110063 restraints weight = 28986.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.110898 restraints weight = 20930.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.111568 restraints weight = 18909.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.111623 restraints weight = 17274.989| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 21345 Z= 0.321 Angle : 0.747 11.080 29490 Z= 0.394 Chirality : 0.047 0.295 3438 Planarity : 0.005 0.063 3410 Dihedral : 20.359 175.794 4126 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.03 % Favored : 91.85 % Rotamer: Outliers : 6.43 % Allowed : 24.34 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.16), residues: 2379 helix: -0.77 (0.20), residues: 640 sheet: -0.47 (0.25), residues: 456 loop : -2.06 (0.16), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 234 TYR 0.030 0.002 TYR D 12 PHE 0.030 0.003 PHE F 182 TRP 0.013 0.002 TRP F 239 HIS 0.009 0.002 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.32 (21345) covalent geometry : angle 0.74735 / 0.39 (29490) hydrogen bonds : bond 0.04329 / 2.85 ( 707) hydrogen bonds : angle 5.48892 / 3.75 ( 1930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 213 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8167 (tpt-90) cc_final: 0.7960 (tpt-90) REVERT: A 47 TYR cc_start: 0.6703 (t80) cc_final: 0.6407 (t80) REVERT: A 57 GLU cc_start: 0.7135 (mp0) cc_final: 0.6549 (tm-30) REVERT: A 58 GLU cc_start: 0.7785 (pm20) cc_final: 0.7180 (pm20) REVERT: A 83 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6250 (tp30) REVERT: B 226 PHE cc_start: 0.6214 (OUTLIER) cc_final: 0.5828 (m-80) REVERT: C 295 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8464 (mp) REVERT: D 56 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7012 (p0) REVERT: E 133 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8091 (ttm-80) REVERT: E 143 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8067 (mt) REVERT: E 273 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7303 (pp) REVERT: F 111 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7230 (t0) REVERT: G 48 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: G 117 TYR cc_start: 0.7937 (t80) cc_final: 0.7730 (t80) REVERT: G 185 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8589 (pp) REVERT: I 121 TYR cc_start: 0.0728 (OUTLIER) cc_final: -0.1182 (t80) outliers start: 124 outliers final: 93 residues processed: 320 average time/residue: 0.1204 time to fit residues: 63.4544 Evaluate side-chains 311 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 207 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 91 LYS Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 239 TRP Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 121 TYR Chi-restraints excluded: chain I residue 145 PHE Chi-restraints excluded: chain I residue 148 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 219 ASN Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 207 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 chunk 95 optimal weight: 0.0570 chunk 54 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 164 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 HIS ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.150098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.111155 restraints weight = 48867.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.110300 restraints weight = 29201.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.111295 restraints weight = 20720.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.111658 restraints weight = 18565.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.111799 restraints weight = 16682.734| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 21345 Z= 0.287 Angle : 1.059 59.164 29490 Z= 0.628 Chirality : 0.048 0.804 3438 Planarity : 0.006 0.132 3410 Dihedral : 20.368 175.732 4125 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.28 % Favored : 91.59 % Rotamer: Outliers : 5.81 % Allowed : 25.06 % Favored : 69.12 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.16), residues: 2379 helix: -0.77 (0.20), residues: 640 sheet: -0.52 (0.25), residues: 458 loop : -2.06 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 118 TYR 0.031 0.002 TYR D 12 PHE 0.030 0.002 PHE G 200 TRP 0.012 0.002 TRP F 239 HIS 0.009 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.29 (21345) covalent geometry : angle 1.05938 / 0.63 (29490) hydrogen bonds : bond 0.04324 / 2.84 ( 707) hydrogen bonds : angle 5.49358 / 3.75 ( 1930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 209 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8190 (tpt-90) cc_final: 0.7979 (tpt-90) REVERT: A 47 TYR cc_start: 0.6630 (t80) cc_final: 0.6331 (t80) REVERT: A 57 GLU cc_start: 0.7150 (mp0) cc_final: 0.6548 (tm-30) REVERT: A 58 GLU cc_start: 0.7784 (pm20) cc_final: 0.7246 (pm20) REVERT: A 83 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6252 (tp30) REVERT: A 106 PHE cc_start: 0.6224 (OUTLIER) cc_final: 0.5360 (m-80) REVERT: B 226 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5790 (m-80) REVERT: C 295 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8465 (mp) REVERT: D 56 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6998 (p0) REVERT: E 133 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8054 (ttm-80) REVERT: E 143 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8071 (mt) REVERT: E 273 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7284 (pp) REVERT: F 111 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7214 (t0) REVERT: G 48 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: G 117 TYR cc_start: 0.7865 (t80) cc_final: 0.7664 (t80) REVERT: G 185 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8562 (pp) REVERT: I 121 TYR cc_start: 0.0740 (OUTLIER) cc_final: -0.1184 (t80) outliers start: 112 outliers final: 91 residues processed: 307 average time/residue: 0.1103 time to fit residues: 55.7093 Evaluate side-chains 305 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 202 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 TRP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 91 LYS Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 239 TRP Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 121 TYR Chi-restraints excluded: chain I residue 145 PHE Chi-restraints excluded: chain I residue 148 PHE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 219 ASN Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 18 optimal weight: 7.9990 chunk 236 optimal weight: 0.0980 chunk 39 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.150640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.111473 restraints weight = 48842.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.110783 restraints weight = 27607.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.111421 restraints weight = 21209.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.112010 restraints weight = 19028.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.112153 restraints weight = 16703.524| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 21345 Z= 0.243 Angle : 0.914 59.187 29490 Z= 0.513 Chirality : 0.046 0.352 3438 Planarity : 0.006 0.130 3410 Dihedral : 20.367 175.842 4123 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.28 % Favored : 91.59 % Rotamer: Outliers : 5.71 % Allowed : 25.17 % Favored : 69.12 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.16), residues: 2379 helix: -0.72 (0.20), residues: 640 sheet: -0.51 (0.25), residues: 458 loop : -2.07 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 118 TYR 0.036 0.002 TYR D 12 PHE 0.046 0.002 PHE G 200 TRP 0.011 0.002 TRP E 239 HIS 0.009 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.24 (21345) covalent geometry : angle 0.91380 / 0.51 (29490) hydrogen bonds : bond 0.04250 / 2.79 ( 707) hydrogen bonds : angle 5.48454 / 3.74 ( 1930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3573.51 seconds wall clock time: 62 minutes 57.31 seconds (3777.31 seconds total)