Starting phenix.real_space_refine on Mon Jul 6 11:50:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8py2_18009/07_2026/8py2_18009.cif Found real_map, /net/cci-nas-00/data/ceres_data/8py2_18009/07_2026/8py2_18009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8py2_18009/07_2026/8py2_18009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8py2_18009/07_2026/8py2_18009.map" model { file = "/net/cci-nas-00/data/ceres_data/8py2_18009/07_2026/8py2_18009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8py2_18009/07_2026/8py2_18009.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 S 212 5.16 5 Cl 8 4.86 5 C 22752 2.51 5 N 6101 2.21 5 O 6653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35730 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2023 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1937 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Chain: "C" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2022 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "D" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1937 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Chain: "E" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3078 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 354} Chain: "F" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3072 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 354} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2027 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 2 Chain: "H" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1937 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Chain: "I" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2027 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 2 Chain: "J" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1937 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Chain: "K" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3078 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 354} Chain: "L" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3060 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 354} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1888 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 220} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "N" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1876 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 220} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1870 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 220} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1887 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 220} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'X8C': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'X8C': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.71, per 1000 atoms: 0.22 Number of scatterers: 35730 At special positions: 0 Unit cell: (212.898, 169.332, 188.238, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Cl 8 17.00 S 212 16.00 O 6653 8.00 N 6101 7.00 C 22752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.4 seconds 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 C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 122 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 124 " pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 122 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 124 " pdb=" ZN I 401 " pdb="ZN ZN I 401 " - pdb=" NE2 HIS I 122 " pdb="ZN ZN I 401 " - pdb=" NE2 HIS I 124 " 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8496 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 25 sheets defined 40.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 93 through 112 Processing helix chain 'A' and resid 132 through 146 Processing helix chain 'A' and resid 225 through 252 Proline residue: A 236 - end of helix removed outlier: 3.797A pdb=" N ILE A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 279 Processing helix chain 'A' and resid 279 through 311 removed outlier: 3.628A pdb=" N LEU A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 20 Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.502A pdb=" N ASP B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 removed outlier: 4.337A pdb=" N LYS B 89 " --> pdb=" O ASP B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 182 through 193 Processing helix chain 'B' and resid 203 through 252 removed outlier: 3.586A pdb=" N ARG B 207 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 93 through 112 Processing helix chain 'C' and resid 132 through 146 removed outlier: 3.525A pdb=" N MET C 145 " --> pdb=" O MET C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 252 Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 257 through 279 Processing helix chain 'C' and resid 279 through 312 Processing helix chain 'D' and resid 6 through 19 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 106 through 121 Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.683A pdb=" N ASN D 167 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 203 through 252 removed outlier: 3.938A pdb=" N ARG D 207 " --> pdb=" O MET D 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 removed outlier: 3.939A pdb=" N ALA E 6 " --> pdb=" O SER E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 24 removed outlier: 3.779A pdb=" N ILE E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 105 Processing helix chain 'E' and resid 111 through 133 Processing helix chain 'E' and resid 137 through 148 removed outlier: 3.942A pdb=" N GLU E 148 " --> pdb=" O THR E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 230 through 236 removed outlier: 3.638A pdb=" N ALA E 234 " --> pdb=" O GLY E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 283 removed outlier: 3.711A pdb=" N GLN E 252 " --> pdb=" O ASP E 248 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE E 282 " --> pdb=" O PHE E 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 10 removed outlier: 3.996A pdb=" N ALA F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 24 removed outlier: 3.558A pdb=" N ILE F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 Processing helix chain 'F' and resid 111 through 133 removed outlier: 3.627A pdb=" N ARG F 133 " --> pdb=" O CYS F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 148 removed outlier: 3.617A pdb=" N GLU F 148 " --> pdb=" O THR F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 153 removed outlier: 3.649A pdb=" N GLU F 153 " --> pdb=" O PRO F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 230 Processing helix chain 'F' and resid 245 through 283 Proline residue: F 251 - end of helix removed outlier: 4.111A pdb=" N SER F 280 " --> pdb=" O ALA F 276 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS F 281 " --> pdb=" O ALA F 277 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE F 282 " --> pdb=" O PHE F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.699A pdb=" N GLN F 372 " --> pdb=" O THR F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 93 through 112 Processing helix chain 'G' and resid 132 through 146 Processing helix chain 'G' and resid 225 through 252 Proline residue: G 236 - end of helix removed outlier: 3.740A pdb=" N ILE G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 279 Processing helix chain 'G' and resid 279 through 312 Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 76 through 84 Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 106 through 121 Processing helix chain 'H' and resid 182 through 193 Processing helix chain 'H' and resid 203 through 252 removed outlier: 3.775A pdb=" N ARG H 207 " --> pdb=" O MET H 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 27 Processing helix chain 'I' and resid 93 through 112 removed outlier: 3.971A pdb=" N ARG I 106 " --> pdb=" O THR I 102 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU I 107 " --> pdb=" O GLU I 103 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 146 removed outlier: 3.716A pdb=" N MET I 145 " --> pdb=" O MET I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 252 Proline residue: I 236 - end of helix removed outlier: 3.789A pdb=" N ILE I 250 " --> pdb=" O ALA I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 279 Processing helix chain 'I' and resid 279 through 312 Processing helix chain 'J' and resid 6 through 20 Processing helix chain 'J' and resid 76 through 84 Processing helix chain 'J' and resid 106 through 120 Processing helix chain 'J' and resid 182 through 193 Processing helix chain 'J' and resid 203 through 252 removed outlier: 3.581A pdb=" N ARG J 207 " --> pdb=" O MET J 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 10 Processing helix chain 'K' and resid 11 through 13 No H-bonds generated for 'chain 'K' and resid 11 through 13' Processing helix chain 'K' and resid 14 through 24 removed outlier: 3.676A pdb=" N ILE K 18 " --> pdb=" O LEU K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 104 removed outlier: 3.507A pdb=" N ALA K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 132 Processing helix chain 'K' and resid 135 through 148 removed outlier: 3.796A pdb=" N MET K 139 " --> pdb=" O SER K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 153 removed outlier: 3.706A pdb=" N GLU K 153 " --> pdb=" O PRO K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 229 Processing helix chain 'K' and resid 230 through 236 Processing helix chain 'K' and resid 245 through 279 removed outlier: 3.871A pdb=" N TYR K 249 " --> pdb=" O CYS K 245 " (cutoff:3.500A) Proline residue: K 251 - end of helix Processing helix chain 'K' and resid 280 through 282 No H-bonds generated for 'chain 'K' and resid 280 through 282' Processing helix chain 'K' and resid 357 through 365 removed outlier: 4.154A pdb=" N TYR K 365 " --> pdb=" O ARG K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 378 removed outlier: 3.803A pdb=" N GLN K 372 " --> pdb=" O THR K 368 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE K 378 " --> pdb=" O GLN K 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 9 removed outlier: 3.609A pdb=" N ALA L 6 " --> pdb=" O SER L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 24 Processing helix chain 'L' and resid 97 through 105 removed outlier: 4.117A pdb=" N ASN L 101 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 135 removed outlier: 4.156A pdb=" N SER L 130 " --> pdb=" O GLN L 126 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG L 131 " --> pdb=" O PHE L 127 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU L 132 " --> pdb=" O GLN L 128 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU L 134 " --> pdb=" O SER L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 148 Processing helix chain 'L' and resid 148 through 153 removed outlier: 3.512A pdb=" N GLU L 153 " --> pdb=" O PRO L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 230 Processing helix chain 'L' and resid 230 through 236 Processing helix chain 'L' and resid 249 through 277 removed outlier: 3.586A pdb=" N ALA L 277 " --> pdb=" O GLU L 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 283 Processing helix chain 'L' and resid 358 through 365 removed outlier: 4.319A pdb=" N TYR L 365 " --> pdb=" O ARG L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 368 No H-bonds generated for 'chain 'L' and resid 366 through 368' Processing helix chain 'L' and resid 369 through 378 removed outlier: 3.802A pdb=" N PHE L 373 " --> pdb=" O PHE L 369 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLU L 375 " --> pdb=" O PRO L 371 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA L 376 " --> pdb=" O GLN L 372 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE L 378 " --> pdb=" O GLN L 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 137 removed outlier: 4.438A pdb=" N VAL M 123 " --> pdb=" O ASN M 119 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS M 137 " --> pdb=" O ARG M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 removed outlier: 3.622A pdb=" N LEU M 166 " --> pdb=" O ASP M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 194 removed outlier: 3.810A pdb=" N PHE M 187 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 238 removed outlier: 3.762A pdb=" N CYS M 238 " --> pdb=" O LYS M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 269 removed outlier: 3.609A pdb=" N ASP M 263 " --> pdb=" O MET M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 272 No H-bonds generated for 'chain 'M' and resid 270 through 272' Processing helix chain 'M' and resid 293 through 299 removed outlier: 3.736A pdb=" N LEU M 299 " --> pdb=" O ALA M 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 134 removed outlier: 3.916A pdb=" N VAL N 123 " --> pdb=" O ASN N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 169 removed outlier: 3.760A pdb=" N LEU N 166 " --> pdb=" O ASP N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 194 removed outlier: 3.585A pdb=" N LYS N 193 " --> pdb=" O LEU N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 257 through 268 removed outlier: 4.252A pdb=" N TRP N 261 " --> pdb=" O GLU N 257 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS N 262 " --> pdb=" O GLU N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 271 No H-bonds generated for 'chain 'N' and resid 269 through 271' Processing helix chain 'N' and resid 288 through 292 Processing helix chain 'N' and resid 293 through 299 removed outlier: 4.272A pdb=" N LYS N 297 " --> pdb=" O ASN N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 307 through 311 Processing helix chain 'O' and resid 101 through 106 removed outlier: 3.941A pdb=" N SER O 106 " --> pdb=" O SER O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 134 removed outlier: 4.004A pdb=" N VAL O 123 " --> pdb=" O ASN O 119 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR O 134 " --> pdb=" O MET O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 162 through 171 removed outlier: 4.047A pdb=" N LEU O 166 " --> pdb=" O ASP O 162 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR O 171 " --> pdb=" O CYS O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 192 removed outlier: 4.371A pdb=" N LEU O 186 " --> pdb=" O ASN O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 237 Processing helix chain 'O' and resid 249 through 255 removed outlier: 4.231A pdb=" N GLU O 253 " --> pdb=" O HIS O 249 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU O 254 " --> pdb=" O ASN O 250 " (cutoff:3.500A) Processing helix chain 'O' and resid 257 through 269 Processing helix chain 'O' and resid 270 through 272 No H-bonds generated for 'chain 'O' and resid 270 through 272' Processing helix chain 'O' and resid 290 through 297 removed outlier: 3.736A pdb=" N CYS O 294 " --> pdb=" O GLU O 290 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET O 295 " --> pdb=" O LEU O 291 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS O 297 " --> pdb=" O ASN O 293 " (cutoff:3.500A) Processing helix chain 'O' and resid 307 through 311 Processing helix chain 'P' and resid 119 through 134 removed outlier: 3.967A pdb=" N VAL P 123 " --> pdb=" O ASN P 119 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG P 133 " --> pdb=" O GLU P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 162 through 169 removed outlier: 3.815A pdb=" N LEU P 166 " --> pdb=" O ASP P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 194 removed outlier: 4.394A pdb=" N LEU P 186 " --> pdb=" O ASN P 182 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE P 187 " --> pdb=" O LEU P 183 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU P 189 " --> pdb=" O GLY P 185 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS P 193 " --> pdb=" O LEU P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 237 Processing helix chain 'P' and resid 249 through 255 removed outlier: 4.298A pdb=" N GLU P 253 " --> pdb=" O HIS P 249 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU P 254 " --> pdb=" O ASN P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 259 through 269 removed outlier: 4.120A pdb=" N ASP P 263 " --> pdb=" O MET P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 272 No H-bonds generated for 'chain 'P' and resid 270 through 272' Processing helix chain 'P' and resid 287 through 293 removed outlier: 3.708A pdb=" N LEU P 291 " --> pdb=" O PRO P 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 297 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 40 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 76 through 79 current: chain 'A' and resid 150 through 156 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 150 through 156 current: chain 'A' and resid 165 through 175 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 211 through 213 current: chain 'B' and resid 53 through 61 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 53 through 61 current: chain 'B' and resid 126 through 134 removed outlier: 4.124A pdb=" N LEU B 147 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 15 removed outlier: 5.926A pdb=" N VAL C 12 " --> pdb=" O HIS C 217 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL C 219 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU C 14 " --> pdb=" O VAL C 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 35 through 40 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 76 through 79 current: chain 'C' and resid 150 through 159 removed outlier: 5.223A pdb=" N CYS C 156 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU C 169 " --> pdb=" O CYS C 156 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C 158 " --> pdb=" O ARG C 167 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 166 through 170 current: chain 'C' and resid 210 through 213 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 210 through 213 current: chain 'D' and resid 53 through 56 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 53 through 56 current: chain 'D' and resid 126 through 130 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 126 through 130 current: chain 'D' and resid 141 through 148 removed outlier: 8.666A pdb=" N TYR D 145 " --> pdb=" O LEU D 160 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU D 160 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU D 147 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 36 through 41 removed outlier: 3.815A pdb=" N ARG E 36 " --> pdb=" O HIS E 59 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR E 38 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU E 40 " --> pdb=" O ARG E 55 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG E 55 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 155 through 159 Processing sheet with id=AA7, first strand: chain 'E' and resid 202 through 204 removed outlier: 3.784A pdb=" N SER E 204 " --> pdb=" O LYS E 218 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS E 218 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 37 through 41 removed outlier: 5.504A pdb=" N ILE F 37 " --> pdb=" O HIS F 59 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS F 59 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP F 39 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS F 57 " --> pdb=" O ASP F 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 155 through 157 removed outlier: 4.298A pdb=" N ALA F 171 " --> pdb=" O PHE F 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 210 through 213 removed outlier: 4.298A pdb=" N GLU G 210 " --> pdb=" O ILE G 176 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE G 176 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG G 167 " --> pdb=" O PHE G 157 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE G 157 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL G 118 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU G 152 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TRP G 120 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE G 154 " --> pdb=" O TRP G 120 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N HIS G 122 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N CYS G 156 " --> pdb=" O HIS G 122 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL G 117 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLY G 40 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N MET G 35 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLU G 41 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE G 74 " --> pdb=" O GLU G 41 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER G 76 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL G 12 " --> pdb=" O HIS G 217 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL G 219 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU G 14 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 2 through 5 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 2 through 5 current: chain 'H' and resid 53 through 61 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 53 through 61 current: chain 'H' and resid 126 through 131 removed outlier: 4.138A pdb=" N LEU H 147 " --> pdb=" O ILE H 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 157 through 158 current: chain 'I' and resid 71 through 78 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 71 through 78 current: chain 'I' and resid 150 through 160 removed outlier: 3.636A pdb=" N ILE I 153 " --> pdb=" O THR I 171 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE I 157 " --> pdb=" O ARG I 167 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG I 167 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU I 159 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR I 165 " --> pdb=" O GLU I 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 2 through 5 removed outlier: 6.519A pdb=" N ALA J 2 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE J 56 " --> pdb=" O ALA J 2 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER J 4 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ASN J 58 " --> pdb=" O SER J 4 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY J 30 " --> pdb=" O VAL J 91 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL J 91 " --> pdb=" O GLY J 30 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU J 147 " --> pdb=" O ILE J 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 55 through 56 Processing sheet with id=AB5, first strand: chain 'K' and resid 61 through 62 Processing sheet with id=AB6, first strand: chain 'K' and resid 158 through 159 Processing sheet with id=AB7, first strand: chain 'K' and resid 175 through 176 Processing sheet with id=AB8, first strand: chain 'L' and resid 36 through 41 removed outlier: 4.676A pdb=" N LEU L 40 " --> pdb=" O ARG L 55 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ARG L 55 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 172 through 177 removed outlier: 4.325A pdb=" N ALA L 201 " --> pdb=" O LEU L 177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 144 through 148 removed outlier: 3.616A pdb=" N ILE M 97 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL M 147 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL M 216 " --> pdb=" O CYS M 98 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR M 280 " --> pdb=" O PHE M 243 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL M 245 " --> pdb=" O TYR M 280 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL M 282 " --> pdb=" O VAL M 245 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N TYR M 247 " --> pdb=" O VAL M 282 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 110 through 111 removed outlier: 3.868A pdb=" N LEU M 110 " --> pdb=" O THR M 118 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR M 118 " --> pdb=" O LEU M 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'N' and resid 155 through 160 removed outlier: 8.098A pdb=" N LEU N 156 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL N 148 " --> pdb=" O LEU N 156 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLY N 158 " --> pdb=" O LEU N 146 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU N 146 " --> pdb=" O GLY N 158 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR N 160 " --> pdb=" O PHE N 144 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE N 97 " --> pdb=" O ALA N 145 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE N 96 " --> pdb=" O ILE N 214 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR N 213 " --> pdb=" O ASP N 244 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N VAL N 246 " --> pdb=" O THR N 213 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU N 215 " --> pdb=" O VAL N 246 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N TYR N 280 " --> pdb=" O PHE N 243 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL N 245 " --> pdb=" O TYR N 280 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 117 through 118 removed outlier: 3.626A pdb=" N LEU N 110 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU N 111 " --> pdb=" O GLY N 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 95 through 97 removed outlier: 3.571A pdb=" N ILE O 96 " --> pdb=" O ARG O 212 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE O 214 " --> pdb=" O ILE O 96 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TYR O 280 " --> pdb=" O PHE O 243 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL O 245 " --> pdb=" O TYR O 280 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL O 282 " --> pdb=" O VAL O 245 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR O 247 " --> pdb=" O VAL O 282 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 110 through 111 removed outlier: 4.008A pdb=" N LEU O 110 " --> pdb=" O THR O 118 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR O 118 " --> pdb=" O LEU O 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'P' and resid 155 through 160 removed outlier: 8.090A pdb=" N LEU P 156 " --> pdb=" O VAL P 148 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL P 148 " --> pdb=" O LEU P 156 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLY P 158 " --> pdb=" O LEU P 146 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU P 146 " --> pdb=" O GLY P 158 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA P 145 " --> pdb=" O VAL P 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 214 " --> pdb=" O ILE P 96 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS P 98 " --> pdb=" O ILE P 214 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL P 216 " --> pdb=" O CYS P 98 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR P 213 " --> pdb=" O ASP P 244 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL P 246 " --> pdb=" O THR P 213 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU P 215 " --> pdb=" O VAL P 246 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE P 248 " --> pdb=" O LEU P 215 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR P 217 " --> pdb=" O ILE P 248 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TYR P 280 " --> pdb=" O PHE P 243 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL P 245 " --> pdb=" O TYR P 280 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL P 282 " --> pdb=" O VAL P 245 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR P 247 " --> pdb=" O VAL P 282 " (cutoff:3.500A) 1369 hydrogen bonds defined for protein. 3972 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: 6.37 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5936 1.31 - 1.44: 9771 1.44 - 1.56: 20529 1.56 - 1.69: 0 1.69 - 1.82: 320 Bond restraints: 36556 Sorted by residual: bond pdb=" CAF X8C F 401 " pdb=" NAH X8C F 401 " ideal model delta sigma weight residual 1.370 1.455 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CAF X8C D 301 " pdb=" NAH X8C D 301 " ideal model delta sigma weight residual 1.370 1.455 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" CBG X8C D 301 " pdb="CLBH X8C D 301 " ideal model delta sigma weight residual 1.721 1.784 -0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" CBG X8C F 401 " pdb="CLBH X8C F 401 " ideal model delta sigma weight residual 1.721 1.783 -0.062 2.00e-02 2.50e+03 9.48e+00 bond pdb=" CAW X8C F 401 " pdb="CLAY X8C F 401 " ideal model delta sigma weight residual 1.722 1.783 -0.061 2.00e-02 2.50e+03 9.33e+00 ... (remaining 36551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 48938 2.11 - 4.21: 482 4.21 - 6.32: 81 6.32 - 8.43: 23 8.43 - 10.54: 8 Bond angle restraints: 49532 Sorted by residual: angle pdb=" C LYS P 140 " pdb=" CA LYS P 140 " pdb=" CB LYS P 140 " ideal model delta sigma weight residual 117.23 110.81 6.42 1.36e+00 5.41e-01 2.23e+01 angle pdb=" CAI X8C F 401 " pdb=" CAJ X8C F 401 " pdb=" CAK X8C F 401 " ideal model delta sigma weight residual 108.45 118.99 -10.54 3.00e+00 1.11e-01 1.23e+01 angle pdb=" CAI X8C D 301 " pdb=" CAJ X8C D 301 " pdb=" CAK X8C D 301 " ideal model delta sigma weight residual 108.45 118.86 -10.41 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA LYS P 140 " pdb=" C LYS P 140 " pdb=" N SER P 141 " ideal model delta sigma weight residual 119.98 117.06 2.92 8.50e-01 1.38e+00 1.18e+01 angle pdb=" CB MET A 309 " pdb=" CG MET A 309 " pdb=" SD MET A 309 " ideal model delta sigma weight residual 112.70 122.19 -9.49 3.00e+00 1.11e-01 1.00e+01 ... (remaining 49527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 18398 17.97 - 35.93: 2692 35.93 - 53.90: 788 53.90 - 71.87: 169 71.87 - 89.84: 86 Dihedral angle restraints: 22133 sinusoidal: 9057 harmonic: 13076 Sorted by residual: dihedral pdb=" CA PHE F 169 " pdb=" C PHE F 169 " pdb=" N SER F 170 " pdb=" CA SER F 170 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA HIS M 142 " pdb=" C HIS M 142 " pdb=" N GLU M 143 " pdb=" CA GLU M 143 " ideal model delta harmonic sigma weight residual 180.00 158.90 21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA SER N 141 " pdb=" C SER N 141 " pdb=" N HIS N 142 " pdb=" CA HIS N 142 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 22130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3423 0.028 - 0.057: 1278 0.057 - 0.085: 389 0.085 - 0.114: 287 0.114 - 0.142: 80 Chirality restraints: 5457 Sorted by residual: chirality pdb=" CA ILE C 153 " pdb=" N ILE C 153 " pdb=" C ILE C 153 " pdb=" CB ILE C 153 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE G 153 " pdb=" N ILE G 153 " pdb=" C ILE G 153 " pdb=" CB ILE G 153 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE C 74 " pdb=" N ILE C 74 " pdb=" C ILE C 74 " pdb=" CB ILE C 74 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 5454 not shown) Planarity restraints: 6415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 213 " 0.018 2.00e-02 2.50e+03 1.50e-02 4.51e+00 pdb=" CG TYR H 213 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR H 213 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR H 213 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR H 213 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR H 213 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR H 213 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 213 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 214 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 215 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 281 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.57e+00 pdb=" N PRO G 282 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO G 282 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 282 " 0.026 5.00e-02 4.00e+02 ... (remaining 6412 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 362 2.58 - 3.16: 29149 3.16 - 3.74: 58601 3.74 - 4.32: 76395 4.32 - 4.90: 127364 Nonbonded interactions: 291871 Sorted by model distance: nonbonded pdb=" OD2 ASP C 135 " pdb="ZN ZN C 401 " model vdw 1.998 2.230 nonbonded pdb=" OD2 ASP I 135 " pdb="ZN ZN I 401 " model vdw 2.025 2.230 nonbonded pdb=" OD2 ASP A 135 " pdb="ZN ZN A 401 " model vdw 2.064 2.230 nonbonded pdb=" OD2 ASP G 135 " pdb="ZN ZN G 401 " model vdw 2.083 2.230 nonbonded pdb=" OH TYR H 173 " pdb=" OE2 GLU I 243 " model vdw 2.122 3.040 ... (remaining 291866 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 7 through 265 or (resid 266 and (name N or name CA or name \ C or name O or name CB )) or resid 267 through 401)) selection = chain 'C' selection = (chain 'G' and (resid 7 through 86 or (resid 87 and (name N or name CA or name C \ or name O or name CB )) or resid 88 through 265 or (resid 266 and (name N or na \ me CA or name C or name O or name CB )) or resid 267 through 401)) selection = (chain 'I' and (resid 7 through 86 or (resid 87 and (name N or name CA or name C \ or name O or name CB )) or resid 88 through 265 or (resid 266 and (name N or na \ me CA or name C or name O or name CB )) or resid 267 through 401)) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 1 through 252) selection = chain 'H' selection = chain 'J' } ncs_group { reference = (chain 'E' and (resid 1 through 223 or (resid 224 and (name N or name CA or name \ C or name O or name CB )) or resid 225 through 299 or (resid 300 and (name N or \ name CA or name C or name O or name CB )) or resid 301 through 307 or (resid 30 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 309 through \ 315 or (resid 316 and (name N or name CA or name C or name O or name CB )) or re \ sid 317 through 351 or (resid 352 and (name N or name CA or name C or name O or \ name CB )) or resid 353 through 383)) selection = (chain 'F' and (resid 1 through 299 or (resid 300 and (name N or name CA or name \ C or name O or name CB )) or resid 301 through 307 or (resid 308 and (name N or \ name CA or name C or name O or name CB )) or resid 309 through 315 or (resid 31 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 317 through \ 351 or (resid 352 and (name N or name CA or name C or name O or name CB )) or re \ sid 353 through 383)) selection = (chain 'K' and (resid 1 through 223 or (resid 224 and (name N or name CA or name \ C or name O or name CB )) or resid 225 through 299 or (resid 300 and (name N or \ name CA or name C or name O or name CB )) or resid 301 through 307 or (resid 30 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 309 through \ 315 or (resid 316 and (name N or name CA or name C or name O or name CB )) or re \ sid 317 through 351 or (resid 352 and (name N or name CA or name C or name O or \ name CB )) or resid 353 through 383)) selection = (chain 'L' and (resid 1 through 223 or (resid 224 and (name N or name CA or name \ C or name O or name CB )) or resid 225 through 383)) } ncs_group { reference = (chain 'M' and (resid 81 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB )) or resid 102 through 135 or (resid 136 through 137 a \ nd (name N or name CA or name C or name O or name CB )) or resid 138 through 141 \ or (resid 142 and (name N or name CA or name C or name O or name CB )) or resid \ 143 through 229 or (resid 230 through 231 and (name N or name CA or name C or n \ ame O or name CB )) or resid 232 through 298 or (resid 299 through 300 and (name \ N or name CA or name C or name O or name CB )) or resid 301 through 313 or (res \ id 314 and (name N or name CA or name C or name O or name CB )) or resid 315 thr \ ough 317)) selection = (chain 'N' and (resid 81 through 135 or (resid 136 through 137 and (name N or na \ me CA or name C or name O or name CB )) or resid 138 through 141 or (resid 142 a \ nd (name N or name CA or name C or name O or name CB )) or resid 143 through 313 \ or (resid 314 and (name N or name CA or name C or name O or name CB )) or resid \ 315 through 317)) selection = (chain 'O' and (resid 81 through 229 or (resid 230 through 231 and (name N or na \ me CA or name C or name O or name CB )) or resid 232 through 298 or (resid 299 t \ hrough 300 and (name N or name CA or name C or name O or name CB )) or resid 301 \ through 317)) selection = (chain 'P' and (resid 81 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB )) or resid 102 through 135 or (resid 136 through 137 a \ nd (name N or name CA or name C or name O or name CB )) or resid 138 through 141 \ or (resid 142 and (name N or name CA or name C or name O or name CB )) or resid \ 143 through 229 or (resid 230 through 231 and (name N or name CA or name C or n \ ame O or name CB )) or resid 232 through 298 or (resid 299 through 300 and (name \ N or name CA or name C or name O or name CB )) or resid 301 through 317)) } 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=0.85 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.820 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 34.180 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5311 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 : 0.003 0.085 36564 Z= 0.135 Angle : 0.540 10.537 49532 Z= 0.264 Chirality : 0.040 0.142 5457 Planarity : 0.003 0.064 6415 Dihedral : 19.142 89.836 13637 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.30 % Allowed : 34.90 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 4380 helix: 1.78 (0.13), residues: 1556 sheet: -1.01 (0.22), residues: 596 loop : -1.24 (0.14), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 36 TYR 0.037 0.001 TYR H 213 PHE 0.030 0.001 PHE P 267 TRP 0.017 0.001 TRP E 105 HIS 0.009 0.001 HIS M 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (36556) covalent geometry : angle 0.54003 / 0.26 (49532) hydrogen bonds : bond 0.15911 / 11.54 ( 1369) hydrogen bonds : angle 6.06323 / 4.38 ( 3972) metal coordination : bond 0.00090 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 358 MET cc_start: 0.1729 (tpt) cc_final: 0.1107 (tpt) REVERT: L 302 MET cc_start: 0.0708 (mpp) cc_final: -0.1113 (mpp) REVERT: L 358 MET cc_start: 0.0274 (tpt) cc_final: -0.0314 (tpt) REVERT: M 235 MET cc_start: -0.1500 (mmt) cc_final: -0.1829 (mmt) REVERT: M 295 MET cc_start: 0.0812 (pmm) cc_final: 0.0429 (pmm) REVERT: N 131 PHE cc_start: 0.1677 (t80) cc_final: 0.1449 (t80) REVERT: N 232 MET cc_start: 0.0881 (tpt) cc_final: -0.0245 (mtt) REVERT: N 235 MET cc_start: -0.1741 (pmm) cc_final: -0.3093 (mtt) REVERT: O 235 MET cc_start: -0.4760 (ttt) cc_final: -0.5052 (tmm) REVERT: O 268 MET cc_start: -0.4286 (OUTLIER) cc_final: -0.6158 (ppp) REVERT: P 232 MET cc_start: -0.1970 (tpt) cc_final: -0.2725 (tpt) REVERT: P 295 MET cc_start: -0.2922 (mmt) cc_final: -0.3880 (mmt) outliers start: 12 outliers final: 2 residues processed: 160 average time/residue: 0.2142 time to fit residues: 58.4044 Evaluate side-chains 127 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain H residue 154 TYR Chi-restraints excluded: chain O residue 268 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 0.0040 overall best weight: 5.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN F 126 GLN G 73 HIS ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 ASN ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.064855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.047087 restraints weight = 248262.545| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 4.38 r_work: 0.3334 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36564 Z= 0.190 Angle : 0.564 9.959 49532 Z= 0.286 Chirality : 0.041 0.152 5457 Planarity : 0.004 0.058 6415 Dihedral : 5.179 78.377 4849 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.20 % Allowed : 31.53 % Favored : 65.27 % 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: -0.12 (0.13), residues: 4380 helix: 1.83 (0.13), residues: 1610 sheet: -0.99 (0.22), residues: 595 loop : -1.33 (0.14), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 133 TYR 0.031 0.001 TYR H 213 PHE 0.032 0.001 PHE P 267 TRP 0.015 0.001 TRP E 105 HIS 0.008 0.001 HIS P 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (36556) covalent geometry : angle 0.56390 / 0.29 (49532) hydrogen bonds : bond 0.04209 / 2.97 ( 1369) hydrogen bonds : angle 4.86642 / 3.48 ( 3972) metal coordination : bond 0.00627 / 0.30 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 125 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9321 (ptt) cc_final: 0.9005 (ptt) REVERT: A 81 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8281 (ttm110) REVERT: A 115 MET cc_start: 0.7106 (mmm) cc_final: 0.6863 (mmm) REVERT: A 285 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8615 (tt0) REVERT: B 23 ASP cc_start: 0.7958 (m-30) cc_final: 0.7164 (m-30) REVERT: C 35 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8849 (mtt) REVERT: C 115 MET cc_start: 0.7689 (mmm) cc_final: 0.7229 (mmm) REVERT: E 302 MET cc_start: 0.0416 (tpt) cc_final: -0.0076 (tpt) REVERT: F 1 MET cc_start: 0.5573 (mpp) cc_final: 0.5368 (mpp) REVERT: F 139 MET cc_start: 0.9088 (tmm) cc_final: 0.8734 (tpp) REVERT: F 271 ARG cc_start: 0.0777 (OUTLIER) cc_final: 0.0069 (mtt90) REVERT: H 105 MET cc_start: 0.8549 (mtp) cc_final: 0.8254 (tpp) REVERT: H 164 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8593 (p0) REVERT: I 149 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.6427 (t80) REVERT: J 1 MET cc_start: 0.5264 (mpp) cc_final: 0.4285 (mmt) REVERT: K 302 MET cc_start: 0.4886 (mmp) cc_final: 0.4125 (mmp) REVERT: L 302 MET cc_start: 0.2207 (mpp) cc_final: 0.1538 (mpp) REVERT: L 358 MET cc_start: -0.0541 (tpt) cc_final: -0.0824 (tpt) REVERT: N 232 MET cc_start: -0.0932 (tpt) cc_final: -0.2660 (mtt) REVERT: N 235 MET cc_start: -0.5486 (pmm) cc_final: -0.6701 (mtt) REVERT: P 232 MET cc_start: -0.4581 (tpt) cc_final: -0.4830 (tpt) REVERT: P 295 MET cc_start: -0.5176 (mmt) cc_final: -0.5429 (mmt) outliers start: 127 outliers final: 46 residues processed: 246 average time/residue: 0.2078 time to fit residues: 85.9164 Evaluate side-chains 175 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 123 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 160 ASP Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 PHE Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 218 GLU Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 227 HIS Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 227 HIS Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 267 PHE Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 248 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 333 optimal weight: 50.0000 chunk 101 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 390 optimal weight: 0.0060 chunk 72 optimal weight: 20.0000 chunk 383 optimal weight: 30.0000 chunk 184 optimal weight: 6.9990 chunk 225 optimal weight: 8.9990 chunk 409 optimal weight: 30.0000 chunk 231 optimal weight: 7.9990 overall best weight: 5.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 GLN ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN G 13 HIS H 57 HIS H 164 ASN ** I 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 294 ASN ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 ASN ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.064318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.045164 restraints weight = 253423.732| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 4.45 r_work: 0.3229 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 36564 Z= 0.185 Angle : 0.550 9.998 49532 Z= 0.278 Chirality : 0.040 0.155 5457 Planarity : 0.004 0.056 6415 Dihedral : 5.077 79.272 4842 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.77 % Allowed : 30.52 % Favored : 65.70 % 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: -0.03 (0.13), residues: 4380 helix: 1.95 (0.13), residues: 1611 sheet: -1.05 (0.22), residues: 609 loop : -1.27 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 133 TYR 0.035 0.001 TYR H 213 PHE 0.024 0.001 PHE P 267 TRP 0.014 0.001 TRP M 261 HIS 0.008 0.001 HIS P 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (36556) covalent geometry : angle 0.55015 / 0.28 (49532) hydrogen bonds : bond 0.03970 / 2.78 ( 1369) hydrogen bonds : angle 4.68866 / 3.34 ( 3972) metal coordination : bond 0.00576 / 0.27 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 126 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9247 (ptt) cc_final: 0.8898 (ptt) REVERT: A 81 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8412 (ttm110) REVERT: A 93 SER cc_start: 0.9470 (OUTLIER) cc_final: 0.9120 (p) REVERT: A 115 MET cc_start: 0.7482 (mmm) cc_final: 0.7081 (mmm) REVERT: A 141 MET cc_start: 0.8720 (tmm) cc_final: 0.8503 (tmm) REVERT: A 285 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8614 (tt0) REVERT: C 35 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8899 (mtt) REVERT: C 115 MET cc_start: 0.8110 (mmm) cc_final: 0.7552 (mmm) REVERT: D 1 MET cc_start: 0.6822 (mpp) cc_final: 0.5754 (mmp) REVERT: E 302 MET cc_start: 0.0347 (tpt) cc_final: -0.0117 (tpt) REVERT: F 170 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8419 (t) REVERT: G 141 MET cc_start: 0.9106 (tmm) cc_final: 0.8346 (tmm) REVERT: H 105 MET cc_start: 0.8625 (mtp) cc_final: 0.8350 (tpp) REVERT: H 139 SER cc_start: 0.9332 (OUTLIER) cc_final: 0.8902 (m) REVERT: H 203 MET cc_start: 0.8916 (tpp) cc_final: 0.8566 (tpp) REVERT: I 149 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6406 (t80) REVERT: I 261 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8926 (mtmm) REVERT: J 1 MET cc_start: 0.5550 (mpp) cc_final: 0.4623 (mmt) REVERT: J 96 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.9000 (mtp85) REVERT: K 1 MET cc_start: 0.5749 (tmm) cc_final: 0.2928 (pmm) REVERT: K 154 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8127 (p0) REVERT: K 302 MET cc_start: 0.5001 (mmp) cc_final: 0.4234 (mmp) REVERT: L 302 MET cc_start: 0.2280 (mpp) cc_final: 0.1576 (mpp) REVERT: L 358 MET cc_start: -0.0632 (tpt) cc_final: -0.0865 (tpt) REVERT: M 235 MET cc_start: -0.2607 (mmm) cc_final: -0.2848 (mmp) REVERT: N 235 MET cc_start: -0.5384 (pmm) cc_final: -0.5723 (mtt) REVERT: O 235 MET cc_start: -0.6450 (tmm) cc_final: -0.6899 (ttt) REVERT: P 232 MET cc_start: -0.4593 (tpt) cc_final: -0.4840 (tpt) outliers start: 150 outliers final: 80 residues processed: 269 average time/residue: 0.2071 time to fit residues: 95.0055 Evaluate side-chains 214 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 124 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 160 ASP Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 149 PHE Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 218 GLU Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 154 ASN Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 227 HIS Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 279 LEU Chi-restraints excluded: chain K residue 308 PHE Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 227 HIS Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 303 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 214 optimal weight: 9.9990 chunk 42 optimal weight: 0.0270 chunk 405 optimal weight: 50.0000 chunk 163 optimal weight: 8.9990 chunk 118 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 overall best weight: 3.2244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN D 137 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 123 GLN ** I 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.064487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.046086 restraints weight = 253097.323| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 5.05 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36564 Z= 0.136 Angle : 0.531 12.732 49532 Z= 0.266 Chirality : 0.040 0.156 5457 Planarity : 0.003 0.055 6415 Dihedral : 5.021 79.442 4842 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.62 % Allowed : 30.05 % Favored : 66.33 % 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: 0.05 (0.13), residues: 4380 helix: 2.03 (0.13), residues: 1616 sheet: -1.01 (0.22), residues: 617 loop : -1.24 (0.14), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 88 TYR 0.024 0.001 TYR H 213 PHE 0.020 0.001 PHE P 267 TRP 0.013 0.001 TRP E 105 HIS 0.008 0.001 HIS P 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (36556) covalent geometry : angle 0.53062 / 0.27 (49532) hydrogen bonds : bond 0.03726 / 2.60 ( 1369) hydrogen bonds : angle 4.54317 / 3.24 ( 3972) metal coordination : bond 0.00327 / 0.15 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 123 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8750 (ptt) cc_final: 0.8241 (ptt) REVERT: A 81 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8115 (ttm110) REVERT: A 93 SER cc_start: 0.9373 (OUTLIER) cc_final: 0.9042 (p) REVERT: A 285 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8433 (tt0) REVERT: C 115 MET cc_start: 0.7600 (mmm) cc_final: 0.7242 (mmm) REVERT: D 1 MET cc_start: 0.6626 (mpp) cc_final: 0.5596 (mmp) REVERT: E 187 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.6719 (p90) REVERT: E 302 MET cc_start: -0.0673 (tpt) cc_final: -0.1193 (tpt) REVERT: F 139 MET cc_start: 0.8946 (tmm) cc_final: 0.8677 (tpp) REVERT: G 234 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8937 (tp30) REVERT: H 105 MET cc_start: 0.8298 (mtp) cc_final: 0.7918 (tpp) REVERT: H 203 MET cc_start: 0.8969 (tpp) cc_final: 0.8686 (tpp) REVERT: I 35 MET cc_start: 0.8474 (mpp) cc_final: 0.7843 (mpp) REVERT: I 149 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6102 (t80) REVERT: I 261 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8770 (mtmm) REVERT: J 1 MET cc_start: 0.5396 (mpp) cc_final: 0.4624 (mpp) REVERT: K 154 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.7995 (p0) REVERT: K 302 MET cc_start: 0.4055 (mmp) cc_final: 0.3167 (mmp) REVERT: L 302 MET cc_start: 0.1411 (mpp) cc_final: 0.0693 (mpp) REVERT: L 358 MET cc_start: -0.1645 (tpt) cc_final: -0.1853 (tpt) REVERT: M 235 MET cc_start: -0.2680 (mmm) cc_final: -0.2914 (mmp) REVERT: N 235 MET cc_start: -0.5331 (pmm) cc_final: -0.6084 (mtt) REVERT: O 235 MET cc_start: -0.6642 (tmm) cc_final: -0.7102 (ttt) REVERT: P 232 MET cc_start: -0.4980 (tpt) cc_final: -0.5199 (tpt) outliers start: 144 outliers final: 84 residues processed: 259 average time/residue: 0.1928 time to fit residues: 85.9621 Evaluate side-chains 215 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 123 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 PHE Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 154 ASN Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 227 HIS Chi-restraints excluded: chain K residue 308 PHE Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 227 HIS Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 310 HIS Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 248 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 275 optimal weight: 0.0470 chunk 137 optimal weight: 30.0000 chunk 299 optimal weight: 10.0000 chunk 359 optimal weight: 10.0000 chunk 355 optimal weight: 1.9990 chunk 284 optimal weight: 0.9990 chunk 325 optimal weight: 0.6980 chunk 131 optimal weight: 50.0000 chunk 124 optimal weight: 6.9990 chunk 394 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.064575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.046807 restraints weight = 249344.607| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 4.30 r_work: 0.3275 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36564 Z= 0.113 Angle : 0.519 9.504 49532 Z= 0.258 Chirality : 0.040 0.156 5457 Planarity : 0.003 0.056 6415 Dihedral : 4.949 79.284 4842 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.52 % Allowed : 29.72 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 4380 helix: 2.11 (0.13), residues: 1616 sheet: -0.92 (0.22), residues: 624 loop : -1.20 (0.14), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 82 TYR 0.021 0.001 TYR H 213 PHE 0.018 0.001 PHE P 267 TRP 0.012 0.001 TRP E 105 HIS 0.011 0.001 HIS P 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (36556) covalent geometry : angle 0.51933 / 0.26 (49532) hydrogen bonds : bond 0.03542 / 2.46 ( 1369) hydrogen bonds : angle 4.42068 / 3.15 ( 3972) metal coordination : bond 0.00219 / 0.10 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 124 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9234 (ptt) cc_final: 0.8812 (ptt) REVERT: A 81 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8580 (ttm110) REVERT: A 155 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8585 (p) REVERT: C 115 MET cc_start: 0.8273 (mmm) cc_final: 0.7746 (mmm) REVERT: D 1 MET cc_start: 0.6746 (mpp) cc_final: 0.5577 (mmp) REVERT: E 187 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6767 (p90) REVERT: E 302 MET cc_start: 0.0061 (tpt) cc_final: -0.0394 (tpt) REVERT: F 139 MET cc_start: 0.9135 (tmm) cc_final: 0.8772 (tpp) REVERT: F 170 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.8053 (t) REVERT: G 234 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8921 (tp30) REVERT: H 105 MET cc_start: 0.8682 (mtp) cc_final: 0.8186 (tpp) REVERT: H 203 MET cc_start: 0.8883 (tpp) cc_final: 0.8506 (tpp) REVERT: I 35 MET cc_start: 0.8712 (mpp) cc_final: 0.8185 (mpp) REVERT: I 149 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6204 (t80) REVERT: I 261 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8906 (mtmm) REVERT: J 1 MET cc_start: 0.5274 (mpp) cc_final: 0.4457 (mpp) REVERT: K 134 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8799 (mt-10) REVERT: K 302 MET cc_start: 0.4887 (mmp) cc_final: 0.4061 (mmp) REVERT: L 302 MET cc_start: 0.2161 (mpp) cc_final: 0.1491 (mpp) REVERT: N 235 MET cc_start: -0.5482 (pmm) cc_final: -0.6273 (mtt) REVERT: O 235 MET cc_start: -0.6496 (tmm) cc_final: -0.6924 (ttt) REVERT: P 232 MET cc_start: -0.4618 (OUTLIER) cc_final: -0.4844 (tpt) outliers start: 140 outliers final: 99 residues processed: 253 average time/residue: 0.1922 time to fit residues: 84.4885 Evaluate side-chains 232 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 124 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 PHE Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 261 LYS Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 227 HIS Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 279 LEU Chi-restraints excluded: chain K residue 308 PHE Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 227 HIS Chi-restraints excluded: chain L residue 236 HIS Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 310 HIS Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 294 CYS Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 214 ILE Chi-restraints excluded: chain P residue 232 MET Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 303 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 178 optimal weight: 5.9990 chunk 410 optimal weight: 20.0000 chunk 379 optimal weight: 0.0070 chunk 255 optimal weight: 7.9990 chunk 357 optimal weight: 50.0000 chunk 194 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 430 optimal weight: 40.0000 chunk 397 optimal weight: 8.9990 chunk 213 optimal weight: 20.0000 overall best weight: 5.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN H 59 HIS ** I 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.063879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.044763 restraints weight = 256637.815| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.32 r_work: 0.3213 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36564 Z= 0.188 Angle : 0.562 11.379 49532 Z= 0.280 Chirality : 0.040 0.165 5457 Planarity : 0.003 0.055 6415 Dihedral : 4.998 80.229 4842 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.72 % Allowed : 29.29 % Favored : 66.99 % 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: 0.12 (0.13), residues: 4380 helix: 2.08 (0.13), residues: 1620 sheet: -0.88 (0.21), residues: 666 loop : -1.25 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 70 TYR 0.020 0.001 TYR H 213 PHE 0.015 0.001 PHE P 267 TRP 0.011 0.001 TRP E 105 HIS 0.009 0.001 HIS P 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (36556) covalent geometry : angle 0.56218 / 0.28 (49532) hydrogen bonds : bond 0.03664 / 2.55 ( 1369) hydrogen bonds : angle 4.48112 / 3.19 ( 3972) metal coordination : bond 0.00649 / 0.30 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 123 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9243 (ptt) cc_final: 0.8809 (ptt) REVERT: A 81 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8310 (ttm110) REVERT: A 285 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: C 115 MET cc_start: 0.8357 (mmm) cc_final: 0.7804 (mmm) REVERT: D 1 MET cc_start: 0.6683 (mpp) cc_final: 0.5624 (mpp) REVERT: E 1 MET cc_start: 0.2096 (pmm) cc_final: 0.1021 (mmt) REVERT: E 187 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6910 (p90) REVERT: E 302 MET cc_start: 0.0849 (tpt) cc_final: 0.0426 (tpt) REVERT: F 170 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8142 (t) REVERT: G 234 GLU cc_start: 0.9302 (OUTLIER) cc_final: 0.8953 (tp30) REVERT: H 105 MET cc_start: 0.8650 (mtp) cc_final: 0.8394 (tpp) REVERT: H 203 MET cc_start: 0.8734 (tpp) cc_final: 0.8408 (tpp) REVERT: I 35 MET cc_start: 0.8772 (mpp) cc_final: 0.8209 (mpp) REVERT: I 149 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.6206 (t80) REVERT: J 1 MET cc_start: 0.5566 (mpp) cc_final: 0.4755 (mpp) REVERT: J 203 MET cc_start: 0.8726 (mmm) cc_final: 0.8497 (mmm) REVERT: K 56 PHE cc_start: 0.9575 (OUTLIER) cc_final: 0.8816 (p90) REVERT: K 134 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8779 (mt-10) REVERT: K 154 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.7982 (p0) REVERT: K 302 MET cc_start: 0.5356 (mmp) cc_final: 0.4597 (mmp) REVERT: L 302 MET cc_start: 0.2664 (mpp) cc_final: 0.1759 (mpp) REVERT: N 235 MET cc_start: -0.5458 (pmm) cc_final: -0.6211 (mtt) REVERT: O 235 MET cc_start: -0.6265 (tmm) cc_final: -0.6707 (ttt) REVERT: P 232 MET cc_start: -0.4204 (OUTLIER) cc_final: -0.4419 (tpt) outliers start: 148 outliers final: 109 residues processed: 265 average time/residue: 0.1815 time to fit residues: 83.2199 Evaluate side-chains 242 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 123 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 PHE Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 56 PHE Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 154 ASN Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 227 HIS Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 279 LEU Chi-restraints excluded: chain K residue 308 PHE Chi-restraints excluded: chain K residue 329 SER Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 227 HIS Chi-restraints excluded: chain L residue 236 HIS Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 357 GLU Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 310 HIS Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 294 CYS Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 214 ILE Chi-restraints excluded: chain P residue 232 MET Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 303 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 418 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 380 optimal weight: 0.9990 chunk 226 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 325 optimal weight: 0.8980 chunk 398 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 chunk 339 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.064230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.045110 restraints weight = 254514.934| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 4.40 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36564 Z= 0.134 Angle : 0.546 12.511 49532 Z= 0.269 Chirality : 0.040 0.171 5457 Planarity : 0.003 0.058 6415 Dihedral : 4.972 80.413 4842 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.60 % Allowed : 29.42 % Favored : 66.99 % 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: 0.14 (0.13), residues: 4380 helix: 2.11 (0.13), residues: 1621 sheet: -0.93 (0.21), residues: 642 loop : -1.22 (0.14), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 70 TYR 0.019 0.001 TYR K 274 PHE 0.014 0.001 PHE P 267 TRP 0.012 0.001 TRP E 105 HIS 0.012 0.001 HIS P 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (36556) covalent geometry : angle 0.54573 / 0.27 (49532) hydrogen bonds : bond 0.03532 / 2.46 ( 1369) hydrogen bonds : angle 4.39323 / 3.13 ( 3972) metal coordination : bond 0.00349 / 0.15 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 124 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8714 (ptt) cc_final: 0.8289 (ptt) REVERT: A 81 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8496 (ttm110) REVERT: A 93 SER cc_start: 0.9395 (OUTLIER) cc_final: 0.9064 (p) REVERT: A 285 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: C 115 MET cc_start: 0.7924 (mmm) cc_final: 0.7467 (mmm) REVERT: C 234 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8892 (tm-30) REVERT: D 203 MET cc_start: 0.8389 (tpp) cc_final: 0.7964 (mmm) REVERT: E 1 MET cc_start: 0.1257 (pmm) cc_final: 0.0368 (mpp) REVERT: E 187 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6621 (p90) REVERT: E 302 MET cc_start: -0.0538 (tpt) cc_final: -0.1062 (tpt) REVERT: F 139 MET cc_start: 0.8943 (tmm) cc_final: 0.8588 (tpp) REVERT: F 170 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.8090 (t) REVERT: G 234 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8900 (tp30) REVERT: H 203 MET cc_start: 0.8796 (tpp) cc_final: 0.8584 (tpp) REVERT: I 35 MET cc_start: 0.8532 (mpp) cc_final: 0.7958 (mpp) REVERT: I 149 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6158 (t80) REVERT: J 1 MET cc_start: 0.5633 (mpp) cc_final: 0.4839 (mmt) REVERT: K 134 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8555 (mt-10) REVERT: K 154 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.7215 (p0) REVERT: K 302 MET cc_start: 0.3714 (mmp) cc_final: 0.2793 (mmp) REVERT: L 302 MET cc_start: 0.1766 (mpp) cc_final: 0.0809 (mpp) REVERT: N 127 MET cc_start: -0.1722 (ppp) cc_final: -0.2292 (ptt) REVERT: O 235 MET cc_start: -0.6612 (tmm) cc_final: -0.7028 (ttt) outliers start: 143 outliers final: 107 residues processed: 257 average time/residue: 0.2031 time to fit residues: 90.1024 Evaluate side-chains 239 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 122 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 PHE Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 154 ASN Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 227 HIS Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 279 LEU Chi-restraints excluded: chain K residue 308 PHE Chi-restraints excluded: chain K residue 329 SER Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 227 HIS Chi-restraints excluded: chain L residue 236 HIS Chi-restraints excluded: chain L residue 256 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 357 GLU Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 310 HIS Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 294 CYS Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 248 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 62 optimal weight: 10.0000 chunk 326 optimal weight: 50.0000 chunk 267 optimal weight: 2.9990 chunk 398 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 323 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 276 optimal weight: 0.4980 chunk 377 optimal weight: 50.0000 chunk 106 optimal weight: 7.9990 overall best weight: 6.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN C 303 GLN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 HIS ** I 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.063705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.044597 restraints weight = 254613.695| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.39 r_work: 0.3204 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 36564 Z= 0.214 Angle : 0.601 12.567 49532 Z= 0.297 Chirality : 0.041 0.231 5457 Planarity : 0.004 0.060 6415 Dihedral : 5.087 81.860 4842 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.55 % Allowed : 29.42 % Favored : 67.04 % 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: 0.03 (0.13), residues: 4380 helix: 2.00 (0.13), residues: 1621 sheet: -1.00 (0.21), residues: 648 loop : -1.25 (0.14), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 271 TYR 0.020 0.001 TYR H 213 PHE 0.014 0.001 PHE P 267 TRP 0.012 0.001 TRP E 105 HIS 0.008 0.001 HIS P 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (36556) covalent geometry : angle 0.60069 / 0.30 (49532) hydrogen bonds : bond 0.03767 / 2.64 ( 1369) hydrogen bonds : angle 4.52978 / 3.23 ( 3972) metal coordination : bond 0.00746 / 0.35 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 123 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9292 (ptt) cc_final: 0.8879 (ptt) REVERT: A 81 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8342 (ttm110) REVERT: A 93 SER cc_start: 0.9421 (OUTLIER) cc_final: 0.9044 (p) REVERT: A 229 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9326 (tp) REVERT: A 285 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: C 115 MET cc_start: 0.8414 (mmm) cc_final: 0.7776 (mmm) REVERT: D 1 MET cc_start: 0.6152 (pmm) cc_final: 0.5151 (mpp) REVERT: D 203 MET cc_start: 0.8489 (tpp) cc_final: 0.8106 (tmm) REVERT: E 1 MET cc_start: 0.2001 (pmm) cc_final: 0.0925 (mpp) REVERT: E 187 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6882 (p90) REVERT: E 195 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8243 (p0) REVERT: E 302 MET cc_start: 0.0178 (tpt) cc_final: -0.0309 (tpt) REVERT: F 170 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.8165 (t) REVERT: G 234 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.8951 (tp30) REVERT: H 203 MET cc_start: 0.8759 (tpp) cc_final: 0.8499 (tpp) REVERT: I 35 MET cc_start: 0.8788 (mpp) cc_final: 0.8224 (mpp) REVERT: I 149 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.6396 (t80) REVERT: J 1 MET cc_start: 0.5820 (mpp) cc_final: 0.5018 (mmt) REVERT: K 13 MET cc_start: 0.8760 (ptt) cc_final: 0.8515 (tmm) REVERT: K 56 PHE cc_start: 0.9565 (OUTLIER) cc_final: 0.8774 (p90) REVERT: K 134 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8760 (mt-10) REVERT: K 154 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.7966 (p0) REVERT: K 302 MET cc_start: 0.5111 (mmp) cc_final: 0.4312 (mmp) REVERT: L 302 MET cc_start: 0.2505 (mpp) cc_final: 0.1530 (mpp) REVERT: N 232 MET cc_start: -0.0194 (tpt) cc_final: -0.2125 (mtt) REVERT: N 235 MET cc_start: -0.5414 (pmm) cc_final: -0.6598 (mtt) REVERT: O 235 MET cc_start: -0.6336 (tmm) cc_final: -0.6808 (ttt) outliers start: 141 outliers final: 108 residues processed: 255 average time/residue: 0.1987 time to fit residues: 87.6732 Evaluate side-chains 243 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 123 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 160 ASP Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 PHE Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 56 PHE Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 154 ASN Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 227 HIS Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 279 LEU Chi-restraints excluded: chain K residue 308 PHE Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 227 HIS Chi-restraints excluded: chain L residue 236 HIS Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 310 HIS Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 294 CYS Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 214 ILE Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 303 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 314 optimal weight: 0.0770 chunk 110 optimal weight: 0.0870 chunk 113 optimal weight: 9.9990 chunk 330 optimal weight: 50.0000 chunk 190 optimal weight: 0.8980 chunk 393 optimal weight: 5.9990 chunk 299 optimal weight: 0.4980 chunk 354 optimal weight: 50.0000 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 20.0000 chunk 243 optimal weight: 5.9990 overall best weight: 1.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 GLN ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.064316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.045185 restraints weight = 252578.414| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.46 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36564 Z= 0.106 Angle : 0.561 13.848 49532 Z= 0.274 Chirality : 0.041 0.217 5457 Planarity : 0.003 0.056 6415 Dihedral : 4.977 81.071 4842 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.77 % Allowed : 30.22 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.13), residues: 4380 helix: 2.13 (0.13), residues: 1606 sheet: -1.01 (0.21), residues: 674 loop : -1.15 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 271 TYR 0.020 0.001 TYR K 274 PHE 0.014 0.001 PHE P 267 TRP 0.015 0.001 TRP E 105 HIS 0.019 0.001 HIS P 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (36556) covalent geometry : angle 0.56085 / 0.27 (49532) hydrogen bonds : bond 0.03497 / 2.44 ( 1369) hydrogen bonds : angle 4.39487 / 3.13 ( 3972) metal coordination : bond 0.00158 / 0.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 125 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8664 (ptt) cc_final: 0.8256 (ptt) REVERT: A 93 SER cc_start: 0.9392 (OUTLIER) cc_final: 0.9051 (p) REVERT: C 115 MET cc_start: 0.7951 (mmm) cc_final: 0.7503 (mmm) REVERT: C 234 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8865 (tm-30) REVERT: D 1 MET cc_start: 0.6212 (pmm) cc_final: 0.5207 (mpp) REVERT: D 203 MET cc_start: 0.8361 (tpp) cc_final: 0.7999 (tmm) REVERT: E 1 MET cc_start: 0.1331 (pmm) cc_final: 0.0290 (mpp) REVERT: E 187 TYR cc_start: 0.7275 (OUTLIER) cc_final: 0.6533 (p90) REVERT: E 302 MET cc_start: -0.0782 (tpt) cc_final: -0.1335 (tpt) REVERT: G 234 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8853 (tp30) REVERT: I 35 MET cc_start: 0.8456 (mpp) cc_final: 0.7967 (mpp) REVERT: I 144 MET cc_start: 0.9207 (ptp) cc_final: 0.8882 (mmt) REVERT: I 149 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.6181 (t80) REVERT: I 285 GLN cc_start: 0.9467 (OUTLIER) cc_final: 0.9214 (tt0) REVERT: J 1 MET cc_start: 0.5830 (mpp) cc_final: 0.5064 (mpp) REVERT: J 33 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8652 (ttp80) REVERT: K 134 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8480 (mt-10) REVERT: K 154 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.7170 (p0) REVERT: K 302 MET cc_start: 0.3610 (mmp) cc_final: 0.2677 (mmp) REVERT: L 198 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5337 (pm20) REVERT: L 302 MET cc_start: 0.1729 (mpp) cc_final: 0.0747 (mpp) REVERT: N 232 MET cc_start: -0.0004 (tpt) cc_final: -0.2041 (mtt) REVERT: N 235 MET cc_start: -0.5194 (pmm) cc_final: -0.6301 (mtt) REVERT: O 235 MET cc_start: -0.6560 (tmm) cc_final: -0.6996 (ttt) outliers start: 110 outliers final: 92 residues processed: 228 average time/residue: 0.2083 time to fit residues: 81.6332 Evaluate side-chains 224 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 122 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 PHE Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 285 GLN Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 151 TYR Chi-restraints excluded: chain K residue 154 ASN Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 227 HIS Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 279 LEU Chi-restraints excluded: chain K residue 308 PHE Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 198 GLU Chi-restraints excluded: chain L residue 227 HIS Chi-restraints excluded: chain L residue 236 HIS Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 310 HIS Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 294 CYS Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 214 ILE Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 303 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 306 optimal weight: 10.0000 chunk 416 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 314 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 87 optimal weight: 0.3980 chunk 206 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN A 285 GLN ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN ** I 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 GLN ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.064167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.045963 restraints weight = 253047.630| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.34 r_work: 0.3310 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36564 Z= 0.105 Angle : 0.567 13.687 49532 Z= 0.276 Chirality : 0.041 0.191 5457 Planarity : 0.003 0.062 6415 Dihedral : 4.905 80.474 4842 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.69 % Allowed : 30.32 % Favored : 66.99 % 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: 0.20 (0.13), residues: 4380 helix: 2.14 (0.13), residues: 1606 sheet: -0.89 (0.21), residues: 674 loop : -1.14 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 271 TYR 0.037 0.001 TYR M 247 PHE 0.014 0.001 PHE P 267 TRP 0.014 0.001 TRP E 105 HIS 0.014 0.001 HIS P 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (36556) covalent geometry : angle 0.56743 / 0.28 (49532) hydrogen bonds : bond 0.03414 / 2.38 ( 1369) hydrogen bonds : angle 4.32348 / 3.08 ( 3972) metal coordination : bond 0.00173 / 0.07 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8760 Ramachandran restraints generated. 4380 Oldfield, 0 Emsley, 4380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 121 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9288 (ptt) cc_final: 0.8875 (ptt) REVERT: A 285 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: C 115 MET cc_start: 0.8408 (mmm) cc_final: 0.7833 (mmm) REVERT: C 145 MET cc_start: 0.9282 (tmm) cc_final: 0.8575 (ppp) REVERT: C 234 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.9010 (tm-30) REVERT: D 1 MET cc_start: 0.6144 (pmm) cc_final: 0.5015 (mpp) REVERT: D 203 MET cc_start: 0.8331 (tpp) cc_final: 0.7855 (tmm) REVERT: E 1 MET cc_start: 0.1416 (pmm) cc_final: 0.0512 (mpp) REVERT: E 155 MET cc_start: 0.8219 (tpt) cc_final: 0.7971 (tpt) REVERT: E 187 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6758 (p90) REVERT: E 302 MET cc_start: 0.0259 (tpt) cc_final: -0.0213 (tpt) REVERT: G 234 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8889 (tp30) REVERT: I 35 MET cc_start: 0.8725 (mpp) cc_final: 0.8240 (mpp) REVERT: I 115 MET cc_start: 0.8113 (mmt) cc_final: 0.7439 (mmm) REVERT: I 144 MET cc_start: 0.9252 (ptp) cc_final: 0.8956 (mmt) REVERT: I 149 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6179 (t80) REVERT: J 1 MET cc_start: 0.5541 (mpp) cc_final: 0.4735 (mpp) REVERT: J 33 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8571 (ttp80) REVERT: K 134 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8662 (mt-10) REVERT: K 154 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.7399 (p0) REVERT: K 302 MET cc_start: 0.5156 (mmp) cc_final: 0.4362 (mmp) REVERT: L 198 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.5987 (pm20) REVERT: L 302 MET cc_start: 0.2448 (mpp) cc_final: 0.1482 (mpp) REVERT: N 127 MET cc_start: -0.1220 (ppp) cc_final: -0.1831 (ptt) REVERT: N 232 MET cc_start: -0.0252 (tpt) cc_final: -0.2117 (mtt) REVERT: N 235 MET cc_start: -0.5350 (pmm) cc_final: -0.6544 (mtt) REVERT: O 235 MET cc_start: -0.6326 (tmm) cc_final: -0.6759 (ttt) outliers start: 107 outliers final: 88 residues processed: 221 average time/residue: 0.2076 time to fit residues: 78.7914 Evaluate side-chains 218 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 121 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 162 LYS Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 149 PHE Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 256 LEU Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 107 TYR Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 151 TYR Chi-restraints excluded: chain K residue 154 ASN Chi-restraints excluded: chain K residue 163 ASN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 191 ASP Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 227 HIS Chi-restraints excluded: chain K residue 256 LEU Chi-restraints excluded: chain K residue 279 LEU Chi-restraints excluded: chain K residue 308 PHE Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 370 VAL Chi-restraints excluded: chain L residue 198 GLU Chi-restraints excluded: chain L residue 227 HIS Chi-restraints excluded: chain L residue 236 HIS Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 136 HIS Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 249 HIS Chi-restraints excluded: chain M residue 310 HIS Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 294 CYS Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 214 ILE Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 303 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 62 optimal weight: 5.9990 chunk 420 optimal weight: 9.9990 chunk 410 optimal weight: 0.0980 chunk 97 optimal weight: 5.9990 chunk 399 optimal weight: 40.0000 chunk 344 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 294 optimal weight: 20.0000 chunk 385 optimal weight: 30.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 GLN ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.063632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.045663 restraints weight = 251331.166| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 4.32 r_work: 0.3296 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36564 Z= 0.138 Angle : 0.570 12.242 49532 Z= 0.278 Chirality : 0.040 0.221 5457 Planarity : 0.003 0.060 6415 Dihedral : 4.893 80.701 4842 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.69 % Allowed : 30.35 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 4380 helix: 2.20 (0.13), residues: 1606 sheet: -0.87 (0.21), residues: 674 loop : -1.14 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 271 TYR 0.021 0.001 TYR M 247 PHE 0.014 0.001 PHE P 267 TRP 0.013 0.001 TRP A 286 HIS 0.013 0.001 HIS P 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (36556) covalent geometry : angle 0.57039 / 0.28 (49532) hydrogen bonds : bond 0.03458 / 2.41 ( 1369) hydrogen bonds : angle 4.32048 / 3.08 ( 3972) metal coordination : bond 0.00426 / 0.19 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11019.85 seconds wall clock time: 188 minutes 33.24 seconds (11313.24 seconds total)