Starting phenix.real_space_refine on Sat Sep 12 05:57:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sqw_55119/09_2026/9sqw_55119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sqw_55119/09_2026/9sqw_55119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sqw_55119/09_2026/9sqw_55119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sqw_55119/09_2026/9sqw_55119.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sqw_55119/09_2026/9sqw_55119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sqw_55119/09_2026/9sqw_55119.map" } resolution = 3.2 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= 0.001 sd= 0.026 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 Zn 2 6.06 5 S 66 5.16 5 C 8707 2.51 5 N 2374 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13761 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2036 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 4, 'TRANS': 249} Chain: "H" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "G" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "J" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "I" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 589 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1914 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 4, 'TRANS': 233} Chain breaks: 1 Chain: "A" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 2057 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 256, 2057 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 2 bond proxies already assigned to first conformer: 2084 Chain: "B" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2004 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 241} Chain breaks: 2 Chain: "E" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1801 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 18, 'TRANS': 209} Chain breaks: 1 Chain: "F" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1547 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N LEU G 73 " occ=0.62 ... (6 atoms not shown) pdb=" CD2 LEU G 73 " occ=0.62 residue: pdb=" N ARG G 74 " occ=0.43 ... (9 atoms not shown) pdb=" NH2 ARG G 74 " occ=0.43 residue: pdb=" N GLY G 75 " occ=0.77 ... (2 atoms not shown) pdb=" O GLY G 75 " occ=0.77 residue: pdb=" N GLY G 76 " occ=0.63 ... (3 atoms not shown) pdb=" OXT GLY G 76 " occ=0.63 residue: pdb=" N ARG J 74 " occ=0.68 ... (9 atoms not shown) pdb=" NH2 ARG J 74 " occ=0.68 residue: pdb=" N GLY J 75 " occ=0.46 ... (2 atoms not shown) pdb=" O GLY J 75 " occ=0.46 Time building chain proxies: 2.94, per 1000 atoms: 0.21 Number of scatterers: 13761 At special positions: 0 Unit cell: (99.16, 119.88, 162.06, 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) Zn 2 29.99 S 66 16.00 O 2612 8.00 N 2374 7.00 C 8707 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 620.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 122 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 124 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 124 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 122 " 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 17 sheets defined 40.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 12 through 25 removed outlier: 3.850A pdb=" N THR C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 111 through 123 Processing helix chain 'C' and resid 156 through 159 Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.508A pdb=" N MET C 173 " --> pdb=" O ASN C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 198 removed outlier: 3.592A pdb=" N HIS C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 256 removed outlier: 3.924A pdb=" N HIS C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 239 " --> pdb=" O ASP C 235 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 34 removed outlier: 3.519A pdb=" N GLN H 31 " --> pdb=" O LYS H 27 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 removed outlier: 3.554A pdb=" N ASP H 58 " --> pdb=" O THR H 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 56 through 60 Processing helix chain 'I' and resid 22 through 35 Processing helix chain 'I' and resid 55 through 60 removed outlier: 3.731A pdb=" N TYR I 59 " --> pdb=" O THR I 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.713A pdb=" N ASN D 24 " --> pdb=" O PHE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 4.027A pdb=" N LYS D 87 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 4.172A pdb=" N LYS D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 174 Processing helix chain 'D' and resid 188 through 198 removed outlier: 3.573A pdb=" N GLN D 196 " --> pdb=" O SER D 192 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.855A pdb=" N PHE D 202 " --> pdb=" O HIS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 257 removed outlier: 3.791A pdb=" N HIS D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 253 " --> pdb=" O ARG D 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 27 Processing helix chain 'A' and resid 93 through 112 removed outlier: 4.501A pdb=" N ALA A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.692A pdb=" N ARG A 137 " --> pdb=" O HIS A 133 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 252 removed outlier: 3.977A pdb=" N LEU A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.538A pdb=" N GLU A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 277 removed outlier: 3.627A pdb=" N SER A 277 " --> pdb=" O CYS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 316 removed outlier: 4.283A pdb=" N GLU A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 301 " --> pdb=" O HIS A 297 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 27 removed outlier: 3.541A pdb=" N VAL B 21 " --> pdb=" O ASP B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 112 Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.613A pdb=" N ALA B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 253 removed outlier: 4.161A pdb=" N LEU B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Proline residue: B 236 - end of helix removed outlier: 3.762A pdb=" N LEU B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 279 Processing helix chain 'B' and resid 279 through 315 removed outlier: 4.088A pdb=" N GLN B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 308 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 313 " --> pdb=" O MET B 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 24 removed outlier: 3.686A pdb=" N SER E 20 " --> pdb=" O PRO E 16 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL E 22 " --> pdb=" O ILE E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 104 removed outlier: 3.509A pdb=" N ALA E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER E 104 " --> pdb=" O GLN E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 104' Processing helix chain 'E' and resid 111 through 133 removed outlier: 3.811A pdb=" N LEU E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL E 116 " --> pdb=" O CYS E 112 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 131 " --> pdb=" O PHE E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 148 removed outlier: 4.017A pdb=" N TYR E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU E 148 " --> pdb=" O THR E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 245 through 247 No H-bonds generated for 'chain 'E' and resid 245 through 247' Processing helix chain 'E' and resid 248 through 254 removed outlier: 3.793A pdb=" N CYS E 254 " --> pdb=" O VAL E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 256 No H-bonds generated for 'chain 'E' and resid 255 through 256' Processing helix chain 'F' and resid 5 through 10 Processing helix chain 'F' and resid 14 through 25 removed outlier: 3.572A pdb=" N ILE F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 98 Processing helix chain 'F' and resid 99 through 104 Processing helix chain 'F' and resid 111 through 134 removed outlier: 3.606A pdb=" N HIS F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN F 126 " --> pdb=" O GLN F 122 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE F 127 " --> pdb=" O GLN F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 147 removed outlier: 3.740A pdb=" N GLU F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 163 through 164 removed outlier: 4.445A pdb=" N LEU C 153 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N VAL C 131 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL C 97 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU C 133 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP C 99 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU C 135 " --> pdb=" O TRP C 99 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS C 101 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU C 33 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TRP C 99 " --> pdb=" O GLY C 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY C 31 " --> pdb=" O TRP C 99 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS C 63 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLU C 36 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE C 61 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LYS C 38 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE C 59 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU C 40 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR C 57 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LYS C 42 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL C 55 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER C 44 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL C 53 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER C 11 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N LYS C 63 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N VAL C 167 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA C 8 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA C 169 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 10 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 163 through 164 removed outlier: 4.445A pdb=" N LEU C 153 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS C 151 " --> pdb=" O GLY B 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 12 through 16 Processing sheet with id=AA4, first strand: chain 'H' and resid 74 through 75 Processing sheet with id=AA5, first strand: chain 'G' and resid 12 through 16 Processing sheet with id=AA6, first strand: chain 'J' and resid 12 through 15 removed outlier: 3.887A pdb=" N LEU J 15 " --> pdb=" O ILE J 3 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE J 3 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE J 4 " --> pdb=" O LEU J 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'I' and resid 12 through 13 Processing sheet with id=AA9, first strand: chain 'I' and resid 44 through 45 Processing sheet with id=AB1, first strand: chain 'D' and resid 147 through 154 removed outlier: 3.651A pdb=" N GLU D 150 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL D 96 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY D 35 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY D 98 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU D 30 " --> pdb=" O CYS D 67 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU D 36 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE D 61 " --> pdb=" O GLU D 36 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LYS D 38 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ILE D 59 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER D 7 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE D 61 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL D 9 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LYS D 63 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N SER D 11 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 13.050A pdb=" N ILE D 65 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA D 8 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA D 169 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU D 10 " --> pdb=" O ALA D 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.256A pdb=" N THR A 165 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU A 159 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ARG A 167 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE A 157 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS A 156 " --> pdb=" O HIS A 124 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS A 38 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TRP A 120 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A 36 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N MET A 35 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A 79 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 37 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL A 77 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 39 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N SER A 76 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 72 through 74 Processing sheet with id=AB4, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.615A pdb=" N SER B 76 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY B 36 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TRP B 120 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N CYS B 38 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LEU B 152 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP B 120 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 36 through 41 removed outlier: 3.674A pdb=" N ARG E 36 " --> pdb=" O HIS E 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR E 38 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS E 57 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU E 40 " --> pdb=" O ARG E 55 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ARG E 55 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 157 through 159 Processing sheet with id=AB7, first strand: chain 'F' and resid 36 through 41 removed outlier: 4.568A pdb=" N LEU F 40 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ARG F 55 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 156 through 158 removed outlier: 3.702A pdb=" N TYR F 158 " --> pdb=" O ARG F 172 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4574 1.34 - 1.46: 2887 1.46 - 1.58: 6453 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 14012 Sorted by residual: bond pdb=" N PRO F 94 " pdb=" CD PRO F 94 " ideal model delta sigma weight residual 1.473 1.291 0.182 1.40e-02 5.10e+03 1.69e+02 bond pdb=" N MET C 187 " pdb=" CA MET C 187 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.08e-02 8.57e+03 7.49e+00 bond pdb=" N LYS D 94 " pdb=" CA LYS D 94 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.34e-02 5.57e+03 7.18e+00 bond pdb=" N TYR C 68 " pdb=" CA TYR C 68 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.34e-02 5.57e+03 7.17e+00 bond pdb=" N VAL B 222 " pdb=" CA VAL B 222 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.22e-02 6.72e+03 6.98e+00 ... (remaining 14007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 18547 1.82 - 3.64: 305 3.64 - 5.46: 48 5.46 - 7.28: 15 7.28 - 9.10: 5 Bond angle restraints: 18920 Sorted by residual: angle pdb=" N LEU A 298 " pdb=" CA LEU A 298 " pdb=" C LEU A 298 " ideal model delta sigma weight residual 113.97 104.87 9.10 1.28e+00 6.10e-01 5.05e+01 angle pdb=" N VAL B 150 " pdb=" CA VAL B 150 " pdb=" CB VAL B 150 " ideal model delta sigma weight residual 112.34 104.60 7.74 1.14e+00 7.69e-01 4.61e+01 angle pdb=" N LEU A 291 " pdb=" CA LEU A 291 " pdb=" C LEU A 291 " ideal model delta sigma weight residual 111.82 105.45 6.37 1.16e+00 7.43e-01 3.02e+01 angle pdb=" N LEU F 93 " pdb=" CA LEU F 93 " pdb=" CB LEU F 93 " ideal model delta sigma weight residual 110.12 101.51 8.61 1.61e+00 3.86e-01 2.86e+01 angle pdb=" C GLN C 69 " pdb=" CA GLN C 69 " pdb=" CB GLN C 69 " ideal model delta sigma weight residual 116.54 110.89 5.65 1.15e+00 7.56e-01 2.42e+01 ... (remaining 18915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7485 17.92 - 35.84: 807 35.84 - 53.76: 212 53.76 - 71.68: 37 71.68 - 89.60: 15 Dihedral angle restraints: 8556 sinusoidal: 3543 harmonic: 5013 Sorted by residual: dihedral pdb=" CD ARG B 167 " pdb=" NE ARG B 167 " pdb=" CZ ARG B 167 " pdb=" NH1 ARG B 167 " ideal model delta sinusoidal sigma weight residual 0.00 72.23 -72.23 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CD ARG A 167 " pdb=" NE ARG A 167 " pdb=" CZ ARG A 167 " pdb=" NH1 ARG A 167 " ideal model delta sinusoidal sigma weight residual 0.00 -54.27 54.27 1 1.00e+01 1.00e-02 3.99e+01 dihedral pdb=" N LEU F 93 " pdb=" C LEU F 93 " pdb=" CA LEU F 93 " pdb=" CB LEU F 93 " ideal model delta harmonic sigma weight residual 122.80 112.17 10.63 0 2.50e+00 1.60e-01 1.81e+01 ... (remaining 8553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1875 0.062 - 0.125: 242 0.125 - 0.187: 23 0.187 - 0.250: 5 0.250 - 0.312: 1 Chirality restraints: 2146 Sorted by residual: chirality pdb=" CA VAL A 34 " pdb=" N VAL A 34 " pdb=" C VAL A 34 " pdb=" CB VAL A 34 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA LEU F 93 " pdb=" N LEU F 93 " pdb=" C LEU F 93 " pdb=" CB LEU F 93 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA VAL B 150 " pdb=" N VAL B 150 " pdb=" C VAL B 150 " pdb=" CB VAL B 150 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2143 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 167 " -1.051 9.50e-02 1.11e+02 4.71e-01 1.34e+02 pdb=" NE ARG B 167 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG B 167 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 167 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 167 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 167 " 0.895 9.50e-02 1.11e+02 4.01e-01 9.77e+01 pdb=" NE ARG A 167 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG A 167 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 167 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 167 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 42 " 0.471 9.50e-02 1.11e+02 2.11e-01 2.73e+01 pdb=" NE ARG J 42 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG J 42 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG J 42 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG J 42 " 0.016 2.00e-02 2.50e+03 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 13 2.12 - 2.81: 3916 2.81 - 3.51: 17277 3.51 - 4.20: 29696 4.20 - 4.90: 52594 Nonbonded interactions: 103496 Sorted by model distance: nonbonded pdb=" NZ LYS H 63 " pdb=" O GLY I 76 " model vdw 1.423 3.120 nonbonded pdb=" CE2 PHE F 169 " pdb=" CB ALA F 171 " model vdw 1.576 3.760 nonbonded pdb=" OE1 GLN F 128 " pdb=" O ILE F 157 " model vdw 1.700 3.040 nonbonded pdb=" CE1 PHE D 112 " pdb=" CG PRO F 94 " model vdw 1.853 3.740 nonbonded pdb=" SD MET E 155 " pdb=" CD1 LEU E 175 " model vdw 1.868 3.820 ... (remaining 103491 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 'A' and (resid 9 through 43 or resid 70 through 72 or resid 74 through 17 \ 7 or resid 210 through 401)) selection = (chain 'B' and (resid 9 through 72 or resid 74 through 401)) } ncs_group { reference = (chain 'C' and (resid 5 through 40 or resid 56 through 257)) selection = chain 'D' } ncs_group { reference = (chain 'G' and (resid 2 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 75 or (resid 76 and (name N or name \ CA or name C or name O )))) selection = (chain 'H' and (resid 2 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 76)) selection = chain 'I' selection = (chain 'J' and (resid 2 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 76)) } 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=0.00 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 12.870 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 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 : 0.005 0.295 14019 Z= 0.418 Angle : 0.586 9.098 18920 Z= 0.349 Chirality : 0.044 0.312 2146 Planarity : 0.014 0.471 2435 Dihedral : 15.944 89.599 5296 Min Nonbonded Distance : 1.423 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.06 % Allowed : 22.20 % Favored : 77.73 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.22), residues: 1689 helix: 0.67 (0.21), residues: 589 sheet: 0.51 (0.29), residues: 383 loop : -0.05 (0.26), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 104 TYR 0.011 0.001 TYR E 249 PHE 0.016 0.001 PHE B 149 TRP 0.009 0.001 TRP C 99 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.24 (14012) covalent geometry : angle 0.58579 / 0.35 (18920) hydrogen bonds : bond 0.26195 / 17.25 ( 594) hydrogen bonds : angle 7.53965 / 5.18 ( 1664) metal coordination : bond 0.00379 / 0.19 ( 4) Misc. bond : bond 0.23661 / 12.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.422 Fit side-chains REVERT: C 14 VAL cc_start: 0.7927 (t) cc_final: 0.7719 (p) REVERT: C 21 GLN cc_start: 0.7593 (tp40) cc_final: 0.7288 (tp40) REVERT: C 42 LYS cc_start: 0.6858 (pttt) cc_final: 0.6594 (pttt) REVERT: C 56 VAL cc_start: 0.7864 (t) cc_final: 0.7582 (m) REVERT: C 95 ASN cc_start: 0.7738 (m-40) cc_final: 0.7438 (m-40) REVERT: C 119 LYS cc_start: 0.7782 (tttt) cc_final: 0.7533 (tttt) REVERT: G 33 LYS cc_start: 0.8713 (tttp) cc_final: 0.8280 (tttp) REVERT: G 48 LYS cc_start: 0.8120 (mttt) cc_final: 0.7905 (mttt) REVERT: D 9 VAL cc_start: 0.8432 (t) cc_final: 0.8066 (p) REVERT: D 205 GLU cc_start: 0.7195 (tp30) cc_final: 0.6893 (tp30) REVERT: A 76 SER cc_start: 0.8300 (p) cc_final: 0.7883 (t) REVERT: A 80 LEU cc_start: 0.8397 (mt) cc_final: 0.8172 (mp) REVERT: B 41 GLU cc_start: 0.7267 (pm20) cc_final: 0.6757 (pm20) REVERT: B 71 ILE cc_start: 0.7947 (pt) cc_final: 0.7627 (pt) REVERT: B 91 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7271 (mt-10) REVERT: B 93 SER cc_start: 0.7614 (m) cc_final: 0.7306 (p) REVERT: B 103 GLU cc_start: 0.7633 (tp30) cc_final: 0.7257 (tp30) REVERT: B 106 ARG cc_start: 0.8209 (tmm-80) cc_final: 0.7811 (tmm-80) REVERT: B 115 MET cc_start: 0.7345 (mmm) cc_final: 0.7115 (mmm) REVERT: B 144 MET cc_start: 0.7308 (mmm) cc_final: 0.7105 (mmm) REVERT: B 167 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7254 (mtm-85) REVERT: F 124 TYR cc_start: 0.8338 (t80) cc_final: 0.8080 (t80) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.1113 time to fit residues: 42.3600 Evaluate side-chains 263 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 HIS C 213 HIS H 49 GLN G 2 GLN D 198 HIS A 143 GLN B 24 ASN B 244 GLN B 255 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.162715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.129889 restraints weight = 38286.386| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.68 r_work: 0.3478 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 0.066 14019 Z= 0.157 Angle : 0.554 7.784 18920 Z= 0.288 Chirality : 0.042 0.145 2146 Planarity : 0.004 0.056 2435 Dihedral : 3.886 19.780 1838 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.96 % Allowed : 21.43 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1689 helix: 1.39 (0.21), residues: 623 sheet: 0.54 (0.29), residues: 370 loop : -0.44 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 211 TYR 0.012 0.001 TYR F 216 PHE 0.019 0.002 PHE F 169 TRP 0.010 0.001 TRP D 99 HIS 0.009 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (14012) covalent geometry : angle 0.55354 / 0.29 (18920) hydrogen bonds : bond 0.05938 / 3.89 ( 594) hydrogen bonds : angle 5.05236 / 3.55 ( 1664) metal coordination : bond 0.00424 / 0.21 ( 4) Misc. bond : bond 0.00158 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 21 GLN cc_start: 0.7656 (tp40) cc_final: 0.7380 (tm-30) REVERT: C 42 LYS cc_start: 0.6802 (pttt) cc_final: 0.6535 (pttt) REVERT: C 62 GLN cc_start: 0.7964 (mt0) cc_final: 0.7563 (mt0) REVERT: C 119 LYS cc_start: 0.8009 (tttt) cc_final: 0.7752 (tttt) REVERT: D 9 VAL cc_start: 0.8488 (t) cc_final: 0.8106 (p) REVERT: A 42 LEU cc_start: 0.7776 (tp) cc_final: 0.7448 (tp) REVERT: A 110 LEU cc_start: 0.8229 (tp) cc_final: 0.7992 (tp) REVERT: B 41 GLU cc_start: 0.7173 (pm20) cc_final: 0.6775 (pm20) REVERT: B 71 ILE cc_start: 0.7967 (pt) cc_final: 0.7604 (pt) REVERT: B 91 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7136 (mt-10) REVERT: B 115 MET cc_start: 0.7230 (mmm) cc_final: 0.6995 (mmm) REVERT: B 139 GLN cc_start: 0.8469 (tp40) cc_final: 0.8200 (tp40) REVERT: B 144 MET cc_start: 0.7221 (mmm) cc_final: 0.6979 (mmm) outliers start: 45 outliers final: 25 residues processed: 301 average time/residue: 0.1085 time to fit residues: 47.3524 Evaluate side-chains 293 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 268 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 156 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 152 optimal weight: 0.4980 chunk 120 optimal weight: 0.6980 chunk 47 optimal weight: 0.0870 chunk 158 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 122 GLN G 2 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN B 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.162711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132814 restraints weight = 21081.126| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.57 r_work: 0.3557 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14019 Z= 0.130 Angle : 0.495 7.388 18920 Z= 0.257 Chirality : 0.041 0.148 2146 Planarity : 0.003 0.042 2435 Dihedral : 3.771 17.452 1838 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.02 % Allowed : 22.20 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.21), residues: 1689 helix: 1.73 (0.21), residues: 622 sheet: 0.50 (0.29), residues: 354 loop : -0.45 (0.25), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 137 TYR 0.010 0.001 TYR F 216 PHE 0.014 0.001 PHE F 169 TRP 0.009 0.001 TRP D 99 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14012) covalent geometry : angle 0.49476 / 0.26 (18920) hydrogen bonds : bond 0.05159 / 3.37 ( 594) hydrogen bonds : angle 4.66216 / 3.28 ( 1664) metal coordination : bond 0.00331 / 0.17 ( 4) Misc. bond : bond 0.00036 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 260 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: C 21 GLN cc_start: 0.7532 (tp40) cc_final: 0.7269 (tm-30) REVERT: C 42 LYS cc_start: 0.6772 (pttt) cc_final: 0.6522 (pttt) REVERT: C 62 GLN cc_start: 0.7855 (mt0) cc_final: 0.7439 (mt0) REVERT: C 119 LYS cc_start: 0.7872 (tttt) cc_final: 0.7659 (tttt) REVERT: C 171 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6865 (tp) REVERT: C 254 ILE cc_start: 0.3978 (OUTLIER) cc_final: 0.3759 (tp) REVERT: D 9 VAL cc_start: 0.8446 (t) cc_final: 0.8061 (p) REVERT: B 41 GLU cc_start: 0.7015 (pm20) cc_final: 0.6576 (pm20) REVERT: B 71 ILE cc_start: 0.7981 (pt) cc_final: 0.7623 (pt) REVERT: B 91 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7086 (mt-10) REVERT: B 115 MET cc_start: 0.7124 (mmm) cc_final: 0.6910 (mmm) REVERT: B 139 GLN cc_start: 0.8442 (tp40) cc_final: 0.8202 (tp40) REVERT: B 144 MET cc_start: 0.7054 (mmm) cc_final: 0.6836 (mmm) REVERT: B 167 ARG cc_start: 0.7623 (mtm-85) cc_final: 0.7234 (mtm-85) REVERT: B 249 ARG cc_start: 0.6809 (mtt90) cc_final: 0.6593 (mtt90) REVERT: F 123 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7694 (mm-40) outliers start: 46 outliers final: 25 residues processed: 288 average time/residue: 0.1132 time to fit residues: 47.3449 Evaluate side-chains 285 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 130 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 157 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 122 GLN H 49 GLN D 81 ASN A 143 GLN A 241 GLN B 24 ASN B 124 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.162735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.130335 restraints weight = 38287.986| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.65 r_work: 0.3472 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14019 Z= 0.156 Angle : 0.513 7.901 18920 Z= 0.263 Chirality : 0.041 0.144 2146 Planarity : 0.003 0.045 2435 Dihedral : 3.873 17.924 1838 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.86 % Allowed : 22.20 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1689 helix: 1.68 (0.21), residues: 632 sheet: 0.46 (0.29), residues: 359 loop : -0.52 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 113 TYR 0.012 0.001 TYR F 62 PHE 0.014 0.002 PHE C 125 TRP 0.008 0.001 TRP A 130 HIS 0.009 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (14012) covalent geometry : angle 0.51311 / 0.26 (18920) hydrogen bonds : bond 0.04894 / 3.19 ( 594) hydrogen bonds : angle 4.51271 / 3.18 ( 1664) metal coordination : bond 0.02749 / 1.37 ( 4) Misc. bond : bond 0.00081 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 265 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 GLN cc_start: 0.7588 (tp40) cc_final: 0.7332 (tm-30) REVERT: C 42 LYS cc_start: 0.6816 (pttt) cc_final: 0.6561 (pttt) REVERT: C 62 GLN cc_start: 0.7937 (mt0) cc_final: 0.7542 (mt0) REVERT: C 119 LYS cc_start: 0.7968 (tttt) cc_final: 0.7739 (tttt) REVERT: C 125 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.5836 (p90) REVERT: C 171 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6805 (tp) REVERT: C 254 ILE cc_start: 0.3976 (OUTLIER) cc_final: 0.3761 (tp) REVERT: D 9 VAL cc_start: 0.8511 (t) cc_final: 0.8128 (p) REVERT: D 79 GLU cc_start: 0.7747 (mp0) cc_final: 0.7341 (mp0) REVERT: D 255 GLU cc_start: 0.3936 (OUTLIER) cc_final: 0.3708 (tm-30) REVERT: B 41 GLU cc_start: 0.7130 (pm20) cc_final: 0.6686 (pm20) REVERT: B 71 ILE cc_start: 0.8049 (pt) cc_final: 0.7701 (pt) REVERT: B 91 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7166 (mt-10) REVERT: B 115 MET cc_start: 0.7201 (mmm) cc_final: 0.6938 (mmm) REVERT: B 139 GLN cc_start: 0.8421 (tp40) cc_final: 0.7968 (tp40) REVERT: B 143 GLN cc_start: 0.7771 (tp40) cc_final: 0.7269 (tp40) REVERT: B 144 MET cc_start: 0.7236 (mmm) cc_final: 0.7009 (mmm) REVERT: B 167 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7390 (mtm-85) REVERT: B 249 ARG cc_start: 0.6981 (mtt90) cc_final: 0.6768 (mtt90) REVERT: E 39 ASP cc_start: 0.5466 (t0) cc_final: 0.5130 (t0) REVERT: E 119 GLU cc_start: 0.7566 (tt0) cc_final: 0.7088 (tt0) REVERT: F 62 TYR cc_start: 0.7135 (t80) cc_final: 0.6635 (t80) REVERT: F 123 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7657 (mm-40) outliers start: 59 outliers final: 42 residues processed: 301 average time/residue: 0.1229 time to fit residues: 53.8582 Evaluate side-chains 307 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 205 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 135 optimal weight: 0.0040 chunk 108 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN B 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.162203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130349 restraints weight = 33121.295| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.39 r_work: 0.3502 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14019 Z= 0.126 Angle : 0.485 8.203 18920 Z= 0.250 Chirality : 0.041 0.145 2146 Planarity : 0.003 0.045 2435 Dihedral : 3.802 17.796 1838 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.67 % Allowed : 22.84 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1689 helix: 1.87 (0.21), residues: 626 sheet: 0.56 (0.30), residues: 346 loop : -0.53 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 131 TYR 0.012 0.001 TYR B 170 PHE 0.011 0.001 PHE C 20 TRP 0.009 0.001 TRP D 99 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (14012) covalent geometry : angle 0.48549 / 0.25 (18920) hydrogen bonds : bond 0.04452 / 2.89 ( 594) hydrogen bonds : angle 4.35723 / 3.07 ( 1664) metal coordination : bond 0.00269 / 0.14 ( 4) Misc. bond : bond 0.00063 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 256 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 GLN cc_start: 0.7594 (tp40) cc_final: 0.7358 (tm-30) REVERT: C 62 GLN cc_start: 0.7904 (mt0) cc_final: 0.7501 (mt0) REVERT: C 125 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.5681 (p90) REVERT: C 171 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6798 (tp) REVERT: C 254 ILE cc_start: 0.3922 (OUTLIER) cc_final: 0.3703 (tp) REVERT: D 9 VAL cc_start: 0.8491 (t) cc_final: 0.8097 (p) REVERT: D 79 GLU cc_start: 0.7658 (mp0) cc_final: 0.7446 (mp0) REVERT: D 205 GLU cc_start: 0.7020 (tp30) cc_final: 0.6741 (tp30) REVERT: D 255 GLU cc_start: 0.3932 (OUTLIER) cc_final: 0.3698 (tm-30) REVERT: B 41 GLU cc_start: 0.7110 (pm20) cc_final: 0.6635 (pm20) REVERT: B 71 ILE cc_start: 0.8070 (pt) cc_final: 0.7721 (pt) REVERT: B 91 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7157 (mt-10) REVERT: B 115 MET cc_start: 0.7190 (mmm) cc_final: 0.6945 (mmm) REVERT: B 139 GLN cc_start: 0.8362 (tp40) cc_final: 0.7968 (tp40) REVERT: B 143 GLN cc_start: 0.7782 (tp40) cc_final: 0.7329 (tp40) REVERT: B 144 MET cc_start: 0.7235 (mmm) cc_final: 0.7015 (mmm) REVERT: B 167 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7403 (mtm-85) REVERT: B 249 ARG cc_start: 0.6927 (mtt90) cc_final: 0.6727 (mtt90) REVERT: E 39 ASP cc_start: 0.5472 (t0) cc_final: 0.5164 (t0) REVERT: F 62 TYR cc_start: 0.7003 (t80) cc_final: 0.6468 (t80) REVERT: F 123 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7677 (mm-40) outliers start: 56 outliers final: 41 residues processed: 290 average time/residue: 0.1239 time to fit residues: 52.5583 Evaluate side-chains 299 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 99 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 39 optimal weight: 0.0470 chunk 32 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 120 ASN H 49 GLN B 24 ASN B 73 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.162191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130828 restraints weight = 32924.841| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.54 r_work: 0.3498 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14019 Z= 0.135 Angle : 0.490 8.578 18920 Z= 0.252 Chirality : 0.041 0.142 2146 Planarity : 0.003 0.046 2435 Dihedral : 3.817 18.298 1838 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.18 % Allowed : 22.52 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.21), residues: 1689 helix: 1.91 (0.21), residues: 626 sheet: 0.44 (0.29), residues: 359 loop : -0.55 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 106 TYR 0.013 0.001 TYR B 170 PHE 0.013 0.001 PHE C 125 TRP 0.008 0.001 TRP D 99 HIS 0.007 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (14012) covalent geometry : angle 0.48970 / 0.25 (18920) hydrogen bonds : bond 0.04415 / 2.87 ( 594) hydrogen bonds : angle 4.31028 / 3.05 ( 1664) metal coordination : bond 0.00390 / 0.20 ( 4) Misc. bond : bond 0.00059 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 262 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 GLN cc_start: 0.7597 (tp40) cc_final: 0.7354 (tm-30) REVERT: C 62 GLN cc_start: 0.7908 (mt0) cc_final: 0.7505 (mt0) REVERT: C 125 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.5578 (p90) REVERT: C 171 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6778 (tp) REVERT: C 254 ILE cc_start: 0.3788 (OUTLIER) cc_final: 0.3575 (tp) REVERT: G 48 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7752 (mmtm) REVERT: D 9 VAL cc_start: 0.8487 (t) cc_final: 0.8086 (p) REVERT: D 205 GLU cc_start: 0.7067 (tp30) cc_final: 0.6782 (tp30) REVERT: D 255 GLU cc_start: 0.3940 (OUTLIER) cc_final: 0.3694 (tm-30) REVERT: B 41 GLU cc_start: 0.7113 (pm20) cc_final: 0.6628 (pm20) REVERT: B 71 ILE cc_start: 0.8074 (pt) cc_final: 0.7732 (pt) REVERT: B 73 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7021 (t-90) REVERT: B 91 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7158 (mt-10) REVERT: B 115 MET cc_start: 0.7195 (mmm) cc_final: 0.6942 (mmm) REVERT: B 139 GLN cc_start: 0.8339 (tp40) cc_final: 0.7971 (tp40) REVERT: B 143 GLN cc_start: 0.7814 (tp40) cc_final: 0.7394 (tp40) REVERT: B 144 MET cc_start: 0.7246 (mmm) cc_final: 0.7020 (mmm) REVERT: B 167 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7396 (mtm-85) REVERT: B 249 ARG cc_start: 0.6966 (mtt90) cc_final: 0.6746 (mtt90) REVERT: E 39 ASP cc_start: 0.5583 (t0) cc_final: 0.5306 (t0) REVERT: F 62 TYR cc_start: 0.6969 (t80) cc_final: 0.6480 (t80) REVERT: F 123 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7709 (mm-40) outliers start: 64 outliers final: 50 residues processed: 305 average time/residue: 0.1164 time to fit residues: 52.1151 Evaluate side-chains 311 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 256 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 205 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 148 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 133 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 GLN B 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.161740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132222 restraints weight = 20884.370| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.56 r_work: 0.3561 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14019 Z= 0.141 Angle : 0.511 9.877 18920 Z= 0.260 Chirality : 0.041 0.142 2146 Planarity : 0.003 0.046 2435 Dihedral : 3.836 18.369 1838 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.73 % Allowed : 23.36 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.21), residues: 1689 helix: 1.88 (0.21), residues: 627 sheet: 0.41 (0.29), residues: 361 loop : -0.55 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 106 TYR 0.037 0.002 TYR E 142 PHE 0.012 0.001 PHE C 125 TRP 0.009 0.001 TRP D 99 HIS 0.015 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (14012) covalent geometry : angle 0.51054 / 0.26 (18920) hydrogen bonds : bond 0.04414 / 2.87 ( 594) hydrogen bonds : angle 4.30742 / 3.04 ( 1664) metal coordination : bond 0.00407 / 0.21 ( 4) Misc. bond : bond 0.00078 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 255 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 21 GLN cc_start: 0.7548 (tp40) cc_final: 0.7313 (tm-30) REVERT: C 62 GLN cc_start: 0.7838 (mt0) cc_final: 0.7427 (mt0) REVERT: C 82 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6958 (mm-30) REVERT: C 125 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.5577 (p90) REVERT: C 171 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6802 (tp) REVERT: C 254 ILE cc_start: 0.3878 (OUTLIER) cc_final: 0.3656 (tp) REVERT: D 9 VAL cc_start: 0.8447 (t) cc_final: 0.8054 (p) REVERT: D 79 GLU cc_start: 0.7670 (mp0) cc_final: 0.7178 (mp0) REVERT: D 205 GLU cc_start: 0.6931 (tp30) cc_final: 0.6669 (tp30) REVERT: D 255 GLU cc_start: 0.3881 (OUTLIER) cc_final: 0.3646 (tm-30) REVERT: B 41 GLU cc_start: 0.7026 (pm20) cc_final: 0.6568 (pm20) REVERT: B 71 ILE cc_start: 0.8039 (pt) cc_final: 0.7707 (pt) REVERT: B 91 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7099 (mt-10) REVERT: B 139 GLN cc_start: 0.8323 (tp40) cc_final: 0.7992 (tp40) REVERT: B 143 GLN cc_start: 0.7770 (tp40) cc_final: 0.7399 (tp40) REVERT: B 167 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7327 (mtm-85) REVERT: B 249 ARG cc_start: 0.6833 (mtt90) cc_final: 0.6610 (mtt90) REVERT: E 39 ASP cc_start: 0.5552 (t0) cc_final: 0.5337 (t0) REVERT: F 62 TYR cc_start: 0.6801 (t80) cc_final: 0.6366 (t80) REVERT: F 123 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7654 (mm-40) outliers start: 57 outliers final: 48 residues processed: 292 average time/residue: 0.1175 time to fit residues: 50.2268 Evaluate side-chains 305 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 252 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 71 optimal weight: 0.9990 chunk 104 optimal weight: 0.0270 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 chunk 155 optimal weight: 0.0970 chunk 149 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 76 optimal weight: 0.5980 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.163344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.133358 restraints weight = 23379.510| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.75 r_work: 0.3556 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14019 Z= 0.102 Angle : 0.510 11.028 18920 Z= 0.254 Chirality : 0.040 0.139 2146 Planarity : 0.003 0.046 2435 Dihedral : 3.715 17.224 1838 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.96 % Allowed : 24.20 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.21), residues: 1689 helix: 1.98 (0.21), residues: 628 sheet: 0.46 (0.29), residues: 360 loop : -0.49 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 131 TYR 0.031 0.001 TYR E 142 PHE 0.010 0.001 PHE B 149 TRP 0.009 0.001 TRP D 99 HIS 0.004 0.001 HIS F 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (14012) covalent geometry : angle 0.51026 / 0.25 (18920) hydrogen bonds : bond 0.04001 / 2.61 ( 594) hydrogen bonds : angle 4.18153 / 2.96 ( 1664) metal coordination : bond 0.00171 / 0.09 ( 4) Misc. bond : bond 0.00031 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: C 21 GLN cc_start: 0.7558 (tp40) cc_final: 0.7331 (tm-30) REVERT: C 62 GLN cc_start: 0.7839 (mt0) cc_final: 0.7428 (mt0) REVERT: C 82 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6950 (mm-30) REVERT: C 125 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.5494 (p90) REVERT: C 254 ILE cc_start: 0.3779 (OUTLIER) cc_final: 0.3554 (tp) REVERT: G 48 LYS cc_start: 0.7782 (mmtm) cc_final: 0.7453 (mmtm) REVERT: D 9 VAL cc_start: 0.8466 (t) cc_final: 0.8063 (p) REVERT: D 79 GLU cc_start: 0.7519 (mp0) cc_final: 0.7100 (mp0) REVERT: D 255 GLU cc_start: 0.3909 (OUTLIER) cc_final: 0.3669 (tm-30) REVERT: B 41 GLU cc_start: 0.7065 (pm20) cc_final: 0.6570 (pm20) REVERT: B 71 ILE cc_start: 0.8056 (pt) cc_final: 0.7735 (pt) REVERT: B 91 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7115 (mt-10) REVERT: B 139 GLN cc_start: 0.8295 (tp40) cc_final: 0.7983 (tp40) REVERT: B 143 GLN cc_start: 0.7792 (tp40) cc_final: 0.7419 (tp40) REVERT: B 167 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7379 (mtm-85) REVERT: E 39 ASP cc_start: 0.5536 (t0) cc_final: 0.5304 (t0) REVERT: F 62 TYR cc_start: 0.6767 (t80) cc_final: 0.6295 (t80) outliers start: 45 outliers final: 33 residues processed: 280 average time/residue: 0.1315 time to fit residues: 53.1232 Evaluate side-chains 288 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN A 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.162635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132107 restraints weight = 26322.079| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.95 r_work: 0.3537 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14019 Z= 0.125 Angle : 0.516 10.391 18920 Z= 0.259 Chirality : 0.041 0.142 2146 Planarity : 0.003 0.046 2435 Dihedral : 3.758 17.936 1838 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.96 % Allowed : 24.32 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1689 helix: 1.98 (0.21), residues: 629 sheet: 0.46 (0.29), residues: 354 loop : -0.52 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 131 TYR 0.024 0.001 TYR E 142 PHE 0.012 0.001 PHE C 125 TRP 0.008 0.001 TRP D 99 HIS 0.007 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (14012) covalent geometry : angle 0.51627 / 0.26 (18920) hydrogen bonds : bond 0.04117 / 2.68 ( 594) hydrogen bonds : angle 4.18122 / 2.96 ( 1664) metal coordination : bond 0.00328 / 0.17 ( 4) Misc. bond : bond 0.00033 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 GLN cc_start: 0.7558 (tp40) cc_final: 0.7336 (tm-30) REVERT: C 62 GLN cc_start: 0.7855 (mt0) cc_final: 0.7445 (mt0) REVERT: C 82 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6914 (mm-30) REVERT: C 125 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.5435 (p90) REVERT: C 254 ILE cc_start: 0.3738 (OUTLIER) cc_final: 0.3514 (tp) REVERT: D 9 VAL cc_start: 0.8475 (t) cc_final: 0.8080 (p) REVERT: D 79 GLU cc_start: 0.7631 (mp0) cc_final: 0.7234 (mp0) REVERT: D 205 GLU cc_start: 0.7001 (tp30) cc_final: 0.6722 (tp30) REVERT: D 255 GLU cc_start: 0.3908 (OUTLIER) cc_final: 0.3669 (tm-30) REVERT: A 212 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7791 (tt) REVERT: B 41 GLU cc_start: 0.7085 (pm20) cc_final: 0.6604 (pm20) REVERT: B 91 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7118 (mt-10) REVERT: B 139 GLN cc_start: 0.8319 (tp40) cc_final: 0.7983 (tp40) REVERT: B 143 GLN cc_start: 0.7789 (tp40) cc_final: 0.7404 (tp40) REVERT: B 249 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6689 (mtt90) REVERT: E 39 ASP cc_start: 0.5598 (t0) cc_final: 0.5347 (t0) REVERT: F 62 TYR cc_start: 0.6737 (t80) cc_final: 0.6326 (t80) outliers start: 45 outliers final: 32 residues processed: 285 average time/residue: 0.1234 time to fit residues: 51.4162 Evaluate side-chains 292 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain F residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 113 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN B 13 HIS B 24 ASN B 217 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.161773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131199 restraints weight = 25870.473| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.92 r_work: 0.3519 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14019 Z= 0.154 Angle : 0.543 10.130 18920 Z= 0.272 Chirality : 0.042 0.144 2146 Planarity : 0.003 0.046 2435 Dihedral : 3.930 18.860 1838 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.64 % Allowed : 24.52 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.21), residues: 1689 helix: 1.91 (0.21), residues: 628 sheet: 0.32 (0.28), residues: 369 loop : -0.54 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 106 TYR 0.018 0.002 TYR E 142 PHE 0.013 0.002 PHE C 112 TRP 0.008 0.001 TRP C 99 HIS 0.008 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (14012) covalent geometry : angle 0.54322 / 0.27 (18920) hydrogen bonds : bond 0.04426 / 2.88 ( 594) hydrogen bonds : angle 4.25238 / 3.00 ( 1664) metal coordination : bond 0.00446 / 0.23 ( 4) Misc. bond : bond 0.00068 / 0.04 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 GLN cc_start: 0.7582 (tp40) cc_final: 0.7337 (tm-30) REVERT: C 62 GLN cc_start: 0.7855 (mt0) cc_final: 0.7449 (mt0) REVERT: C 82 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7032 (mm-30) REVERT: C 125 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.5444 (p90) REVERT: C 254 ILE cc_start: 0.3680 (OUTLIER) cc_final: 0.3453 (tp) REVERT: D 9 VAL cc_start: 0.8489 (t) cc_final: 0.8091 (p) REVERT: D 79 GLU cc_start: 0.7704 (mp0) cc_final: 0.7308 (mp0) REVERT: D 205 GLU cc_start: 0.6981 (tp30) cc_final: 0.6705 (tp30) REVERT: D 255 GLU cc_start: 0.3949 (OUTLIER) cc_final: 0.3713 (tm-30) REVERT: B 41 GLU cc_start: 0.7098 (pm20) cc_final: 0.6613 (pm20) REVERT: B 71 ILE cc_start: 0.7818 (pt) cc_final: 0.7602 (pt) REVERT: B 91 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7125 (mt-10) REVERT: B 139 GLN cc_start: 0.8337 (tp40) cc_final: 0.7953 (tp40) REVERT: B 143 GLN cc_start: 0.7797 (tp40) cc_final: 0.7403 (tp40) REVERT: B 167 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7389 (mtm-85) REVERT: B 249 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6613 (mtt90) REVERT: E 39 ASP cc_start: 0.5850 (t0) cc_final: 0.5617 (t0) REVERT: F 62 TYR cc_start: 0.6718 (t80) cc_final: 0.6300 (t80) outliers start: 40 outliers final: 33 residues processed: 293 average time/residue: 0.1208 time to fit residues: 51.7608 Evaluate side-chains 307 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 236 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 99 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN B 24 ASN B 174 GLN B 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.161615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131536 restraints weight = 26145.075| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.93 r_work: 0.3522 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 902 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14019 Z= 0.144 Angle : 0.545 14.292 18920 Z= 0.270 Chirality : 0.042 0.144 2146 Planarity : 0.003 0.047 2435 Dihedral : 3.935 19.187 1838 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.90 % Allowed : 24.58 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.21), residues: 1689 helix: 1.91 (0.21), residues: 628 sheet: 0.32 (0.28), residues: 369 loop : -0.59 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 131 TYR 0.017 0.001 TYR E 142 PHE 0.012 0.001 PHE C 20 TRP 0.008 0.001 TRP D 99 HIS 0.008 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (14012) covalent geometry : angle 0.54510 / 0.27 (18920) hydrogen bonds : bond 0.04301 / 2.80 ( 594) hydrogen bonds : angle 4.21662 / 2.98 ( 1664) metal coordination : bond 0.00422 / 0.21 ( 4) Misc. bond : bond 0.00074 / 0.04 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3898.98 seconds wall clock time: 67 minutes 34.33 seconds (4054.33 seconds total)