Starting phenix.real_space_refine on Sat Jul 4 11:49:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k28_36831/07_2026/8k28_36831.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k28_36831/07_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_36831/07_2026/8k28_36831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k28_36831/07_2026/8k28_36831.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k28_36831/07_2026/8k28_36831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k28_36831/07_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-dev-6108/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: 4.61, per 1000 atoms: 0.22 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: 1.99 Conformation dependent library (CDL) restraints added in 910.4 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: 2.67 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: 2.46 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: 28916 3.56 - 7.12: 463 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: 3284 0.145 - 0.290: 137 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: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.080 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.020 ------------------------------------------------------------------------------- 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= 0.497 Angle : 1.190 17.793 29490 Z= 0.741 Chirality : 0.071 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 1.19022 / 0.74 (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 : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8382 (tpt170) cc_final: 0.8158 (tpt170) 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: 0.7346 (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: 0.1235 time to fit residues: 67.9866 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 : 0.720 ------------------------------------------------------------------------------- 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: 40.0000 chunk 98 optimal weight: 0.7980 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: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.154103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.111857 restraints weight = 47283.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.112961 restraints weight = 28428.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.114449 restraints weight = 18966.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.115112 restraints weight = 15028.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.115327 restraints weight = 14471.899| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21345 Z= 0.171 Angle : 0.674 10.332 29490 Z= 0.369 Chirality : 0.045 0.246 3438 Planarity : 0.005 0.069 3410 Dihedral : 20.857 175.329 4146 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.64 % Favored : 93.19 % Rotamer: Outliers : 4.77 % Allowed : 23.82 % 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: -2.65 (0.16), residues: 2379 helix: -1.58 (0.18), residues: 625 sheet: -0.78 (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 0.029 0.002 TYR I 91 PHE 0.031 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 0.00353 / 0.17 (21345) covalent geometry : angle 0.67369 / 0.37 (29490) hydrogen bonds : bond 0.04907 / 3.26 ( 707) hydrogen bonds : angle 5.98300 / 4.15 ( 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 : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 PHE cc_start: 0.6445 (t80) cc_final: 0.6110 (t80) REVERT: A 47 TYR cc_start: 0.6602 (t80) cc_final: 0.6389 (t80) REVERT: A 57 GLU cc_start: 0.7175 (mp0) cc_final: 0.6723 (tm-30) REVERT: B 158 CYS cc_start: 0.6105 (OUTLIER) cc_final: 0.5603 (m) REVERT: B 179 LEU cc_start: 0.7010 (tp) cc_final: 0.6771 (tt) REVERT: C 12 TYR cc_start: 0.7125 (m-10) cc_final: 0.6887 (m-10) REVERT: C 172 MET cc_start: 0.6191 (ptp) cc_final: 0.5453 (ptm) REVERT: C 234 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6659 (ttm110) REVERT: C 295 LEU cc_start: 0.8871 (mp) cc_final: 0.8582 (tt) REVERT: E 147 ASP cc_start: 0.6538 (m-30) cc_final: 0.6134 (t0) REVERT: F 267 LYS cc_start: 0.7612 (tttp) cc_final: 0.7410 (mtpp) REVERT: G 48 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: G 268 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7542 (p) REVERT: I 130 LYS cc_start: 0.7981 (pttm) cc_final: 0.7457 (pttp) outliers start: 92 outliers final: 53 residues processed: 316 average time/residue: 0.1150 time to fit residues: 59.9446 Evaluate side-chains 272 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 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 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 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 49 SER 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 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: 0.6980 chunk 150 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 230 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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** ** 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 ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.150240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.107600 restraints weight = 47103.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.108262 restraints weight = 30622.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.109246 restraints weight = 20767.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.109951 restraints weight = 17298.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.109948 restraints weight = 15060.316| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21345 Z= 0.231 Angle : 0.654 9.176 29490 Z= 0.360 Chirality : 0.045 0.267 3438 Planarity : 0.004 0.059 3410 Dihedral : 20.751 175.020 4139 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.40 % Favored : 92.52 % Rotamer: Outliers : 6.12 % Allowed : 22.99 % Favored : 70.89 % 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: -2.29 (0.16), residues: 2379 helix: -1.05 (0.20), residues: 619 sheet: -0.69 (0.24), residues: 489 loop : -2.14 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 118 TYR 0.030 0.002 TYR F 12 PHE 0.024 0.002 PHE A 9 TRP 0.013 0.002 TRP H 28 HIS 0.008 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 (21345) covalent geometry : angle 0.65438 / 0.36 (29490) hydrogen bonds : bond 0.04495 / 2.98 ( 707) hydrogen bonds : angle 5.60993 / 3.87 ( 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 343 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 225 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8088 (mm-30) REVERT: A 165 GLN cc_start: 0.7256 (mp10) cc_final: 0.6871 (mp10) REVERT: B 226 PHE cc_start: 0.5833 (OUTLIER) cc_final: 0.5408 (m-80) REVERT: C 172 MET cc_start: 0.6182 (ptp) cc_final: 0.5451 (ptm) REVERT: C 295 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8540 (mp) REVERT: D 88 ASP cc_start: 0.6340 (t0) cc_final: 0.6099 (t0) REVERT: E 147 ASP cc_start: 0.6645 (m-30) cc_final: 0.6218 (t0) REVERT: E 180 GLU cc_start: 0.6354 (mm-30) cc_final: 0.5996 (mm-30) REVERT: E 273 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7131 (pp) REVERT: G 48 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: G 119 TYR cc_start: 0.8998 (m-80) cc_final: 0.8689 (m-80) REVERT: G 268 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7808 (p) REVERT: G 270 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7958 (tp) REVERT: I 121 TYR cc_start: 0.0588 (OUTLIER) cc_final: -0.0963 (t80) REVERT: I 130 LYS cc_start: 0.7929 (pttm) cc_final: 0.7449 (pttp) REVERT: H 104 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7841 (pt0) outliers start: 118 outliers final: 77 residues processed: 318 average time/residue: 0.1161 time to fit residues: 61.3612 Evaluate side-chains 293 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 209 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 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 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 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 247 ILE Chi-restraints excluded: chain F residue 284 THR 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 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: 5.9990 chunk 21 optimal weight: 0.7980 chunk 198 optimal weight: 0.7980 chunk 225 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 C 227 GLN D 61 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** 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 148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.152096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.109641 restraints weight = 47153.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.111354 restraints weight = 27458.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.112207 restraints weight = 17216.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.112798 restraints weight = 16048.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.112836 restraints weight = 14034.795| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21345 Z= 0.141 Angle : 0.604 10.242 29490 Z= 0.331 Chirality : 0.044 0.269 3438 Planarity : 0.004 0.054 3410 Dihedral : 20.678 176.229 4135 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.85 % Favored : 93.06 % Rotamer: Outliers : 5.60 % Allowed : 23.46 % Favored : 70.94 % 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: -2.10 (0.16), residues: 2379 helix: -0.82 (0.20), residues: 620 sheet: -0.60 (0.24), residues: 479 loop : -2.04 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 234 TYR 0.020 0.001 TYR A 47 PHE 0.021 0.001 PHE E 205 TRP 0.013 0.001 TRP D 130 HIS 0.006 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (21345) covalent geometry : angle 0.60352 / 0.33 (29490) hydrogen bonds : bond 0.04011 / 2.67 ( 707) hydrogen bonds : angle 5.37633 / 3.70 ( 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 342 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 234 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.6370 (t80) cc_final: 0.6043 (t80) REVERT: A 58 GLU cc_start: 0.8053 (pm20) cc_final: 0.7635 (pm20) REVERT: A 70 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8038 (m-40) REVERT: A 83 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6458 (tp30) REVERT: A 165 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6788 (mp10) REVERT: B 226 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5451 (m-80) REVERT: C 234 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7024 (ttm110) REVERT: C 295 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8516 (mp) REVERT: D 56 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7069 (p0) REVERT: D 204 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7350 (mm-30) REVERT: E 147 ASP cc_start: 0.6575 (m-30) cc_final: 0.6220 (t0) REVERT: E 273 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7135 (pp) REVERT: F 111 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7515 (t0) REVERT: G 48 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: G 119 TYR cc_start: 0.8959 (m-80) cc_final: 0.8647 (m-80) REVERT: G 185 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8336 (pp) REVERT: G 268 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7871 (p) REVERT: G 270 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8001 (tp) REVERT: I 121 TYR cc_start: 0.0605 (OUTLIER) cc_final: -0.0911 (t80) REVERT: H 104 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7865 (pt0) REVERT: H 274 MET cc_start: 0.8426 (ttm) cc_final: 0.8047 (ttm) outliers start: 108 outliers final: 68 residues processed: 322 average time/residue: 0.1223 time to fit residues: 64.6778 Evaluate side-chains 299 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 217 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 71 MET 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 183 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 227 GLN 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 56 ASP 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 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 72 HIS Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 142 VAL 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 55 ASN 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 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 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 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 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 278 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 46 optimal weight: 0.0370 chunk 137 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 overall best weight: 2.1464 ------------------------------------------------------------------------------- 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 ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.150430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.107130 restraints weight = 46985.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.109065 restraints weight = 27707.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.109827 restraints weight = 17374.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.110447 restraints weight = 16200.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.110450 restraints weight = 14205.657| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21345 Z= 0.193 Angle : 0.625 9.693 29490 Z= 0.340 Chirality : 0.044 0.268 3438 Planarity : 0.004 0.054 3410 Dihedral : 20.570 176.025 4135 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.23 % Favored : 92.69 % Rotamer: Outliers : 6.64 % Allowed : 22.94 % Favored : 70.42 % 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: -2.02 (0.16), residues: 2379 helix: -0.70 (0.20), residues: 618 sheet: -0.61 (0.24), residues: 479 loop : -2.00 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 133 TYR 0.023 0.002 TYR D 12 PHE 0.021 0.002 PHE I 145 TRP 0.009 0.001 TRP E 239 HIS 0.006 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (21345) covalent geometry : angle 0.62487 / 0.34 (29490) hydrogen bonds : bond 0.04039 / 2.69 ( 707) hydrogen bonds : angle 5.32681 / 3.67 ( 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 349 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 221 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7588 (OUTLIER) cc_final: 0.7320 (m) REVERT: A 47 TYR cc_start: 0.6632 (t80) cc_final: 0.6212 (t80) REVERT: A 58 GLU cc_start: 0.7874 (pm20) cc_final: 0.7508 (pm20) REVERT: A 70 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8254 (m-40) REVERT: A 83 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6367 (tp30) REVERT: A 165 GLN cc_start: 0.7521 (mp10) cc_final: 0.7300 (mp10) REVERT: B 226 PHE cc_start: 0.5866 (OUTLIER) cc_final: 0.5476 (m-80) REVERT: C 172 MET cc_start: 0.6408 (ptp) cc_final: 0.5697 (ptp) REVERT: C 234 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6990 (ttm110) REVERT: C 295 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8531 (mp) REVERT: D 56 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7099 (p0) REVERT: D 204 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7250 (mm-30) REVERT: E 180 GLU cc_start: 0.6211 (mm-30) cc_final: 0.5965 (mm-30) REVERT: E 273 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7200 (pp) REVERT: F 111 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7471 (t0) REVERT: G 48 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: G 119 TYR cc_start: 0.8991 (m-80) cc_final: 0.8717 (m-80) REVERT: G 185 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8355 (pp) REVERT: G 268 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8091 (p) REVERT: G 270 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8042 (tp) REVERT: I 121 TYR cc_start: 0.0407 (OUTLIER) cc_final: -0.1171 (t80) REVERT: H 104 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7857 (pt0) REVERT: H 274 MET cc_start: 0.8463 (ttm) cc_final: 0.8157 (ttm) outliers start: 128 outliers final: 86 residues processed: 321 average time/residue: 0.1156 time to fit residues: 60.9163 Evaluate side-chains 304 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 204 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 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 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 295 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 56 ASP 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 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 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 72 HIS Chi-restraints excluded: chain E residue 82 ASN Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 142 VAL 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 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 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 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 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 193 LEU 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: 7.9990 chunk 61 optimal weight: 0.0570 chunk 76 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.3502 ------------------------------------------------------------------------------- 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 ** 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 78 HIS H 33 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.152874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.113042 restraints weight = 48604.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.113625 restraints weight = 27446.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.114966 restraints weight = 18198.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.115227 restraints weight = 16278.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.115332 restraints weight = 15059.581| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21345 Z= 0.155 Angle : 0.602 9.910 29490 Z= 0.328 Chirality : 0.044 0.273 3438 Planarity : 0.004 0.070 3410 Dihedral : 20.491 176.407 4132 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 6.18 % Allowed : 24.18 % Favored : 69.64 % 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: -1.98 (0.16), residues: 2379 helix: -0.63 (0.20), residues: 625 sheet: -0.59 (0.24), residues: 474 loop : -1.98 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 133 TYR 0.020 0.002 TYR A 47 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 0.00333 / 0.16 (21345) covalent geometry : angle 0.60170 / 0.33 (29490) hydrogen bonds : bond 0.03794 / 2.53 ( 707) hydrogen bonds : angle 5.20360 / 3.58 ( 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 337 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 218 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 47 TYR cc_start: 0.6603 (t80) cc_final: 0.6191 (t80) REVERT: A 58 GLU cc_start: 0.7961 (pm20) cc_final: 0.7540 (pm20) REVERT: A 70 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8047 (t0) REVERT: A 83 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6330 (tp30) REVERT: B 226 PHE cc_start: 0.5971 (OUTLIER) cc_final: 0.5597 (m-80) REVERT: C 12 TYR cc_start: 0.7287 (m-10) cc_final: 0.6894 (m-80) REVERT: C 234 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6934 (ttm110) REVERT: C 295 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8399 (mp) REVERT: D 56 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7207 (p0) REVERT: D 204 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7187 (mm-30) REVERT: E 233 ILE cc_start: 0.9381 (mt) cc_final: 0.9150 (mt) REVERT: E 273 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7135 (pp) REVERT: F 111 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7267 (t0) REVERT: F 294 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8522 (m-40) REVERT: G 48 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: G 119 TYR cc_start: 0.9010 (m-80) cc_final: 0.8743 (m-80) REVERT: G 172 MET cc_start: 0.7530 (ppp) cc_final: 0.7253 (ppp) REVERT: G 185 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8337 (pp) REVERT: G 268 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8215 (p) REVERT: I 121 TYR cc_start: 0.0350 (OUTLIER) cc_final: -0.1273 (t80) REVERT: H 104 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7838 (pt0) REVERT: H 274 MET cc_start: 0.8314 (ttm) cc_final: 0.8018 (ttm) outliers start: 119 outliers final: 84 residues processed: 311 average time/residue: 0.1146 time to fit residues: 59.4055 Evaluate side-chains 302 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 205 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 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 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 234 ARG 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 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 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 72 HIS Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 142 VAL 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 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 256 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 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 78 HIS 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 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 193 LEU 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: 0.9990 chunk 71 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 209 optimal weight: 50.0000 chunk 149 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 216 optimal weight: 50.0000 chunk 98 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 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 18 ASN I 78 HIS 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 = 0.4298 r_free = 0.4298 target = 0.149979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.106830 restraints weight = 46957.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.108288 restraints weight = 26091.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.109228 restraints weight = 18296.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.109949 restraints weight = 15312.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.110171 restraints weight = 13615.921| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21345 Z= 0.194 Angle : 0.630 12.155 29490 Z= 0.340 Chirality : 0.044 0.272 3438 Planarity : 0.004 0.075 3410 Dihedral : 20.401 176.219 4126 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.27 % Favored : 92.64 % Rotamer: Outliers : 6.49 % Allowed : 24.08 % Favored : 69.43 % 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: -1.97 (0.16), residues: 2379 helix: -0.61 (0.21), residues: 620 sheet: -0.57 (0.24), residues: 482 loop : -2.01 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 76 TYR 0.019 0.002 TYR D 12 PHE 0.024 0.001 PHE D 150 TRP 0.010 0.001 TRP E 239 HIS 0.008 0.001 HIS I 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (21345) covalent geometry : angle 0.62964 / 0.34 (29490) hydrogen bonds : bond 0.03834 / 2.53 ( 707) hydrogen bonds : angle 5.25106 / 3.60 ( 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 339 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 214 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.6647 (t80) cc_final: 0.6370 (t80) REVERT: A 58 GLU cc_start: 0.7982 (pm20) cc_final: 0.7608 (pm20) REVERT: A 70 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8161 (m-40) REVERT: B 158 CYS cc_start: 0.6347 (OUTLIER) cc_final: 0.5831 (m) REVERT: B 226 PHE cc_start: 0.6150 (OUTLIER) cc_final: 0.5731 (m-80) REVERT: C 12 TYR cc_start: 0.7279 (m-10) cc_final: 0.6938 (m-80) REVERT: C 295 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8433 (mp) REVERT: D 38 MET cc_start: 0.7929 (mmp) cc_final: 0.7694 (mmp) REVERT: D 56 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7228 (p0) REVERT: D 204 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7217 (mm-30) REVERT: E 233 ILE cc_start: 0.9414 (mt) cc_final: 0.9177 (mt) REVERT: E 273 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7254 (pp) REVERT: F 111 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7250 (t0) REVERT: G 48 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: G 172 MET cc_start: 0.7590 (ppp) cc_final: 0.7285 (ppp) REVERT: G 185 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8363 (pp) REVERT: G 268 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8311 (p) REVERT: I 121 TYR cc_start: 0.0185 (OUTLIER) cc_final: -0.1336 (t80) REVERT: H 104 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7946 (pt0) REVERT: H 274 MET cc_start: 0.8390 (ttm) cc_final: 0.7990 (ttm) outliers start: 125 outliers final: 92 residues processed: 311 average time/residue: 0.1128 time to fit residues: 57.2953 Evaluate side-chains 311 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 208 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 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 70 LYS Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 158 CYS 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 267 LYS 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 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 142 VAL 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 180 GLU 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 256 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 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 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 78 HIS 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 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: 40.0000 chunk 230 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 20.0000 chunk 242 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 196 optimal weight: 8.9990 chunk 229 optimal weight: 0.9990 chunk 41 optimal weight: 0.0170 chunk 133 optimal weight: 2.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- 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 ** 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 78 HIS H 33 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.153150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.109924 restraints weight = 46618.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.111559 restraints weight = 27039.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.112940 restraints weight = 16957.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.113364 restraints weight = 14548.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.113409 restraints weight = 13191.393| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2544 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= 0.149 Angle : 0.616 9.162 29490 Z= 0.331 Chirality : 0.043 0.276 3438 Planarity : 0.004 0.073 3410 Dihedral : 20.373 176.637 4126 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.31 % Favored : 92.60 % Rotamer: Outliers : 5.66 % Allowed : 25.27 % Favored : 69.07 % 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: -1.92 (0.17), residues: 2379 helix: -0.56 (0.21), residues: 619 sheet: -0.48 (0.24), residues: 479 loop : -2.00 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 234 TYR 0.033 0.002 TYR F 12 PHE 0.023 0.001 PHE F 182 TRP 0.012 0.001 TRP E 239 HIS 0.008 0.001 HIS I 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (21345) covalent geometry : angle 0.61574 / 0.33 (29490) hydrogen bonds : bond 0.03644 / 2.41 ( 707) hydrogen bonds : angle 5.18985 / 3.55 ( 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 331 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 222 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 47 TYR cc_start: 0.6579 (t80) cc_final: 0.6280 (t80) REVERT: A 58 GLU cc_start: 0.7954 (pm20) cc_final: 0.7538 (pm20) REVERT: B 13 ASP cc_start: 0.7043 (m-30) cc_final: 0.6808 (t0) REVERT: B 158 CYS cc_start: 0.6391 (OUTLIER) cc_final: 0.5856 (m) REVERT: B 226 PHE cc_start: 0.6165 (OUTLIER) cc_final: 0.5755 (m-80) REVERT: C 12 TYR cc_start: 0.7297 (m-10) cc_final: 0.7014 (m-80) REVERT: C 295 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8454 (mp) REVERT: D 38 MET cc_start: 0.7990 (mmp) cc_final: 0.7694 (mmp) REVERT: D 56 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7281 (p0) REVERT: D 204 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7268 (mm-30) REVERT: E 233 ILE cc_start: 0.9384 (mt) cc_final: 0.9161 (mt) REVERT: E 273 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7196 (pp) REVERT: F 111 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.7014 (t0) REVERT: F 227 GLN cc_start: 0.8154 (pt0) cc_final: 0.7815 (pt0) REVERT: G 48 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: G 172 MET cc_start: 0.7658 (ppp) cc_final: 0.7371 (ppp) REVERT: G 185 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8303 (pp) REVERT: G 268 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8318 (p) REVERT: I 121 TYR cc_start: 0.0201 (OUTLIER) cc_final: -0.1345 (t80) REVERT: H 104 GLN cc_start: 0.8428 (mm-40) cc_final: 0.7935 (pt0) outliers start: 109 outliers final: 86 residues processed: 307 average time/residue: 0.1158 time to fit residues: 58.6966 Evaluate side-chains 306 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 210 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 158 CYS 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 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 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 142 VAL 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 180 GLU 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 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 206 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 233 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 78 HIS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 210 optimal weight: 50.0000 chunk 113 optimal weight: 0.0980 chunk 8 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 186 optimal weight: 0.6980 chunk 236 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 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 I 78 HIS H 33 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.152966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.109768 restraints weight = 46767.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.111668 restraints weight = 26412.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.112701 restraints weight = 17709.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.113239 restraints weight = 14929.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.113558 restraints weight = 13163.844| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 21345 Z= 0.158 Angle : 0.623 8.977 29490 Z= 0.335 Chirality : 0.044 0.276 3438 Planarity : 0.004 0.069 3410 Dihedral : 20.330 176.675 4124 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.31 % Favored : 92.60 % Rotamer: Outliers : 5.76 % Allowed : 25.27 % Favored : 68.97 % 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: -1.90 (0.17), residues: 2379 helix: -0.54 (0.21), residues: 619 sheet: -0.46 (0.24), residues: 479 loop : -1.99 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 234 TYR 0.030 0.002 TYR F 12 PHE 0.029 0.001 PHE D 150 TRP 0.012 0.001 TRP E 239 HIS 0.005 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (21345) covalent geometry : angle 0.62253 / 0.33 (29490) hydrogen bonds : bond 0.03600 / 2.38 ( 707) hydrogen bonds : angle 5.14912 / 3.52 ( 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 331 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 220 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 47 TYR cc_start: 0.6632 (t80) cc_final: 0.6281 (t80) REVERT: A 58 GLU cc_start: 0.7962 (pm20) cc_final: 0.7533 (pm20) REVERT: B 158 CYS cc_start: 0.6349 (OUTLIER) cc_final: 0.5862 (m) REVERT: B 226 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5831 (m-80) REVERT: C 12 TYR cc_start: 0.7355 (m-10) cc_final: 0.7081 (m-80) REVERT: C 295 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8433 (mp) REVERT: D 38 MET cc_start: 0.7873 (mmp) cc_final: 0.7598 (mmp) REVERT: D 56 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7344 (p0) REVERT: D 204 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7266 (mm-30) REVERT: E 233 ILE cc_start: 0.9366 (mt) cc_final: 0.9140 (mt) REVERT: E 273 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7184 (pp) REVERT: F 111 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6952 (t0) REVERT: F 227 GLN cc_start: 0.8159 (pt0) cc_final: 0.7804 (pt0) REVERT: G 48 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: G 172 MET cc_start: 0.7592 (ppp) cc_final: 0.7371 (ppp) REVERT: G 185 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8318 (pp) REVERT: G 268 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8334 (p) REVERT: I 121 TYR cc_start: 0.0220 (OUTLIER) cc_final: -0.1330 (t80) REVERT: H 104 GLN cc_start: 0.8428 (mm-40) cc_final: 0.7962 (pt0) REVERT: H 274 MET cc_start: 0.8286 (ttm) cc_final: 0.8023 (ttm) outliers start: 111 outliers final: 91 residues processed: 311 average time/residue: 0.1128 time to fit residues: 57.7982 Evaluate side-chains 312 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 211 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 70 LYS Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 158 CYS 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 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 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 142 VAL 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 180 GLU 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 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 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 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 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 207 optimal weight: 20.0000 chunk 108 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 180 optimal weight: 0.1980 chunk 40 optimal weight: 20.0000 chunk 164 optimal weight: 0.5980 chunk 181 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 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** I 18 ASN H 33 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 = 0.4345 r_free = 0.4345 target = 0.153389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.110167 restraints weight = 47041.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.111838 restraints weight = 26894.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.113169 restraints weight = 18039.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.113700 restraints weight = 14584.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.113906 restraints weight = 13445.314| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21345 Z= 0.148 Angle : 0.627 9.921 29490 Z= 0.335 Chirality : 0.044 0.278 3438 Planarity : 0.004 0.067 3410 Dihedral : 20.304 176.811 4124 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.36 % Favored : 92.56 % Rotamer: Outliers : 5.55 % Allowed : 25.53 % Favored : 68.92 % 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: -1.87 (0.17), residues: 2379 helix: -0.54 (0.21), residues: 619 sheet: -0.31 (0.25), residues: 444 loop : -1.98 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 234 TYR 0.029 0.002 TYR F 12 PHE 0.027 0.001 PHE D 150 TRP 0.012 0.001 TRP E 239 HIS 0.006 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (21345) covalent geometry : angle 0.62737 / 0.33 (29490) hydrogen bonds : bond 0.03570 / 2.38 ( 707) hydrogen bonds : angle 5.12552 / 3.50 ( 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 327 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 220 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8262 (tpt170) cc_final: 0.8015 (tpt-90) REVERT: A 47 TYR cc_start: 0.6506 (t80) cc_final: 0.6231 (t80) REVERT: A 58 GLU cc_start: 0.7957 (pm20) cc_final: 0.7681 (pm20) REVERT: A 106 PHE cc_start: 0.6050 (OUTLIER) cc_final: 0.5273 (m-80) REVERT: A 131 LEU cc_start: 0.7683 (mp) cc_final: 0.7428 (mp) REVERT: B 158 CYS cc_start: 0.6423 (OUTLIER) cc_final: 0.5858 (m) REVERT: B 226 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5846 (m-80) REVERT: C 12 TYR cc_start: 0.7258 (m-10) cc_final: 0.7046 (m-80) REVERT: C 295 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8411 (mp) REVERT: D 38 MET cc_start: 0.7774 (mmp) cc_final: 0.7492 (mmp) REVERT: D 56 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7270 (p0) REVERT: D 204 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7276 (mm-30) REVERT: E 233 ILE cc_start: 0.9333 (mt) cc_final: 0.9104 (mt) REVERT: E 273 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7104 (pp) REVERT: F 111 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6808 (t0) REVERT: F 227 GLN cc_start: 0.8111 (pt0) cc_final: 0.7722 (pt0) REVERT: G 48 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: G 185 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8336 (pp) REVERT: G 268 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8332 (p) REVERT: I 121 TYR cc_start: 0.0289 (OUTLIER) cc_final: -0.1294 (t80) REVERT: H 104 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7958 (pt0) REVERT: H 274 MET cc_start: 0.8272 (ttm) cc_final: 0.8012 (ttm) outliers start: 107 outliers final: 90 residues processed: 306 average time/residue: 0.1132 time to fit residues: 57.4293 Evaluate side-chains 313 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 212 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET 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 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 74 GLN Chi-restraints excluded: chain B residue 158 CYS 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 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 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 142 VAL 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 153 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 180 GLU 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 141 THR 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 18 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 216 optimal weight: 50.0000 chunk 57 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 243 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.147763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.106288 restraints weight = 46902.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.105160 restraints weight = 33206.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105904 restraints weight = 24599.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.106324 restraints weight = 19854.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.106643 restraints weight = 18463.927| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 21345 Z= 0.327 Angle : 0.740 13.778 29490 Z= 0.395 Chirality : 0.047 0.272 3438 Planarity : 0.005 0.066 3410 Dihedral : 20.336 175.338 4124 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.28 % Favored : 91.59 % Rotamer: Outliers : 5.40 % Allowed : 25.84 % Favored : 68.76 % 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: -2.04 (0.16), residues: 2379 helix: -0.76 (0.20), residues: 632 sheet: -0.48 (0.25), residues: 457 loop : -2.03 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 234 TYR 0.038 0.002 TYR F 12 PHE 0.029 0.003 PHE F 182 TRP 0.030 0.003 TRP B 73 HIS 0.008 0.002 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00723 / 0.33 (21345) covalent geometry : angle 0.74043 / 0.40 (29490) hydrogen bonds : bond 0.04288 / 2.85 ( 707) hydrogen bonds : angle 5.40778 / 3.69 ( 1930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3322.04 seconds wall clock time: 58 minutes 29.46 seconds (3509.46 seconds total)