Starting phenix.real_space_refine on Thu Jan 15 07:46:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vik_32011/01_2026/7vik_32011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vik_32011/01_2026/7vik_32011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vik_32011/01_2026/7vik_32011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vik_32011/01_2026/7vik_32011.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vik_32011/01_2026/7vik_32011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vik_32011/01_2026/7vik_32011.map" } resolution = 3.76 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 15330 2.51 5 N 4137 2.21 5 O 4774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24346 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2669 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 18, 'TRANS': 320} Chain: "B" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2669 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 18, 'TRANS': 320} Chain: "C" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2669 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 18, 'TRANS': 320} Chain: "D" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2669 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 18, 'TRANS': 320} Chain: "E" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2669 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 18, 'TRANS': 320} Chain: "F" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2669 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 18, 'TRANS': 320} Chain: "G" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2669 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 18, 'TRANS': 320} Chain: "H" Number of atoms: 809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} Conformer: "B" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} bond proxies already assigned to first conformer: 821 Chain: "I" Number of atoms: 809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} Conformer: "B" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} bond proxies already assigned to first conformer: 821 Chain: "J" Number of atoms: 809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} Conformer: "B" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} bond proxies already assigned to first conformer: 821 Chain: "K" Number of atoms: 809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} Conformer: "B" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} bond proxies already assigned to first conformer: 821 Chain: "L" Number of atoms: 809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} Conformer: "B" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} bond proxies already assigned to first conformer: 821 Chain: "M" Number of atoms: 809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} Conformer: "B" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} bond proxies already assigned to first conformer: 821 Chain: "N" Number of atoms: 809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} Conformer: "B" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} bond proxies already assigned to first conformer: 821 Time building chain proxies: 7.00, per 1000 atoms: 0.29 Number of scatterers: 24346 At special positions: 0 Unit cell: (223.418, 207.74, 92.7643, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4774 8.00 N 4137 7.00 C 15330 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: 2.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5838 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 63 sheets defined 19.8% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 103 through 138 removed outlier: 3.746A pdb=" N ARG A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.559A pdb=" N ASN A 160 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 161 " --> pdb=" O GLU A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 180 through 188 Processing helix chain 'A' and resid 205 through 211 removed outlier: 3.643A pdb=" N PHE A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.714A pdb=" N LYS A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.739A pdb=" N GLU A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.856A pdb=" N PHE A 335 " --> pdb=" O PRO A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.926A pdb=" N THR B 89 " --> pdb=" O PRO B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 138 removed outlier: 3.532A pdb=" N ARG B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 190 removed outlier: 4.056A pdb=" N ASN B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.609A pdb=" N LYS B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 331 through 335 removed outlier: 4.059A pdb=" N PHE B 335 " --> pdb=" O PRO B 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 removed outlier: 3.796A pdb=" N PHE C 27 " --> pdb=" O PHE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.856A pdb=" N THR C 89 " --> pdb=" O PRO C 86 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 90 " --> pdb=" O GLN C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 138 removed outlier: 3.600A pdb=" N ARG C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET C 129 " --> pdb=" O GLN C 125 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN C 130 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.647A pdb=" N ASN C 160 " --> pdb=" O SER C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.764A pdb=" N PHE C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.765A pdb=" N LYS C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 331 through 335 removed outlier: 3.963A pdb=" N PHE C 335 " --> pdb=" O PRO C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 removed outlier: 3.731A pdb=" N LEU D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE D 27 " --> pdb=" O PHE D 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 22 through 27' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.593A pdb=" N LEU D 90 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG D 91 " --> pdb=" O MET D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 91' Processing helix chain 'D' and resid 105 through 138 removed outlier: 3.651A pdb=" N VAL D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 180 through 190 removed outlier: 4.203A pdb=" N ASN D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 211 removed outlier: 3.692A pdb=" N PHE D 211 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 219 removed outlier: 3.648A pdb=" N LYS D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 Processing helix chain 'D' and resid 331 through 335 removed outlier: 3.768A pdb=" N PHE D 335 " --> pdb=" O PRO D 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 138 Processing helix chain 'E' and resid 157 through 161 Processing helix chain 'E' and resid 180 through 190 removed outlier: 4.351A pdb=" N ASN E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 211 removed outlier: 3.638A pdb=" N PHE E 211 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 219 removed outlier: 3.712A pdb=" N LYS E 215 " --> pdb=" O PHE E 211 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP E 219 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 Processing helix chain 'E' and resid 331 through 335 removed outlier: 3.627A pdb=" N PHE E 335 " --> pdb=" O PRO E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 90 removed outlier: 3.863A pdb=" N THR F 89 " --> pdb=" O PRO F 86 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU F 90 " --> pdb=" O GLN F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 138 removed outlier: 3.529A pdb=" N ARG F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 161 Processing helix chain 'F' and resid 180 through 189 Processing helix chain 'F' and resid 205 through 211 Processing helix chain 'F' and resid 211 through 218 removed outlier: 3.875A pdb=" N LYS F 215 " --> pdb=" O PHE F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 297 Processing helix chain 'F' and resid 331 through 335 removed outlier: 3.819A pdb=" N PHE F 335 " --> pdb=" O PRO F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 138 Processing helix chain 'G' and resid 157 through 161 removed outlier: 3.539A pdb=" N ASN G 160 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN G 161 " --> pdb=" O GLU G 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 157 through 161' Processing helix chain 'G' and resid 180 through 190 removed outlier: 4.507A pdb=" N ASN G 190 " --> pdb=" O ALA G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 211 removed outlier: 4.187A pdb=" N LEU G 207 " --> pdb=" O LYS G 203 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE G 208 " --> pdb=" O GLY G 204 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 215 Processing helix chain 'G' and resid 225 through 234 Processing helix chain 'G' and resid 290 through 296 removed outlier: 3.778A pdb=" N ARG G 295 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU G 296 " --> pdb=" O ASP G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 335 removed outlier: 3.779A pdb=" N PHE G 335 " --> pdb=" O PRO G 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 100 Processing helix chain 'I' and resid 94 through 100 Processing helix chain 'J' and resid 94 through 101 removed outlier: 3.503A pdb=" N LYS J 98 " --> pdb=" O ASP J 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 100 Processing helix chain 'L' and resid 94 through 100 Processing helix chain 'M' and resid 94 through 100 Processing helix chain 'M' and resid 101 through 103 No H-bonds generated for 'chain 'M' and resid 101 through 103' Processing helix chain 'N' and resid 94 through 100 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 9 removed outlier: 6.480A pdb=" N GLN A 8 " --> pdb=" O TYR F 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.605A pdb=" N GLN B 8 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.519A pdb=" N TRP A 308 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 144 removed outlier: 5.586A pdb=" N GLY A 144 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASP A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 228 removed outlier: 5.774A pdb=" N TYR A 241 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL A 252 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 243 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 258 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=AA9, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AB1, first strand: chain 'B' and resid 40 through 43 removed outlier: 8.659A pdb=" N TYR B 40 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA C 12 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N SER B 42 " --> pdb=" O ALA C 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.520A pdb=" N THR B 319 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TRP B 308 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 139 through 144 removed outlier: 6.078A pdb=" N GLY B 144 " --> pdb=" O ASP B 148 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASP B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.976A pdb=" N VAL B 252 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE B 250 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 256 through 258 Processing sheet with id=AB6, first strand: chain 'B' and resid 271 through 274 Processing sheet with id=AB7, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AB8, first strand: chain 'C' and resid 38 through 40 Processing sheet with id=AB9, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.709A pdb=" N HIS C 82 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR C 319 " --> pdb=" O HIS C 82 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 139 through 144 removed outlier: 5.873A pdb=" N GLY C 144 " --> pdb=" O ASP C 148 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 240 through 245 removed outlier: 6.189A pdb=" N ILE C 250 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N MET C 244 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AC4, first strand: chain 'C' and resid 271 through 274 Processing sheet with id=AC5, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AC6, first strand: chain 'D' and resid 38 through 40 Processing sheet with id=AC7, first strand: chain 'D' and resid 82 through 83 removed outlier: 3.814A pdb=" N THR D 319 " --> pdb=" O HIS D 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 139 through 144 removed outlier: 5.681A pdb=" N GLY D 144 " --> pdb=" O ASP D 148 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 243 through 244 removed outlier: 3.714A pdb=" N GLY D 243 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 256 through 258 Processing sheet with id=AD2, first strand: chain 'D' and resid 271 through 274 Processing sheet with id=AD3, first strand: chain 'D' and resid 281 through 285 removed outlier: 4.238A pdb=" N THR D 284 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 38 through 40 Processing sheet with id=AD5, first strand: chain 'E' and resid 139 through 144 removed outlier: 5.864A pdb=" N GLY E 144 " --> pdb=" O ASP E 148 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASP E 148 " --> pdb=" O GLY E 144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 240 through 244 removed outlier: 5.942A pdb=" N TYR E 241 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL E 252 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY E 243 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 256 through 258 Processing sheet with id=AD8, first strand: chain 'E' and resid 271 through 274 Processing sheet with id=AD9, first strand: chain 'E' and resid 281 through 285 removed outlier: 4.220A pdb=" N THR E 284 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 304 through 310 removed outlier: 3.915A pdb=" N ARG E 316 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 82 through 83 removed outlier: 3.710A pdb=" N THR F 319 " --> pdb=" O HIS F 82 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG F 316 " --> pdb=" O THR F 310 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP F 308 " --> pdb=" O PHE F 318 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 139 through 144 removed outlier: 6.151A pdb=" N GLY F 144 " --> pdb=" O ASP F 148 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 243 through 244 removed outlier: 4.023A pdb=" N GLY F 243 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 256 through 258 Processing sheet with id=AE6, first strand: chain 'F' and resid 271 through 274 removed outlier: 3.536A pdb=" N VAL F 336 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 281 through 282 Processing sheet with id=AE8, first strand: chain 'G' and resid 82 through 83 removed outlier: 3.868A pdb=" N ARG G 316 " --> pdb=" O THR G 310 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 139 through 144 removed outlier: 5.679A pdb=" N GLY G 144 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP G 148 " --> pdb=" O GLY G 144 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 239 through 244 removed outlier: 5.265A pdb=" N TYR G 241 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL G 252 " --> pdb=" O TYR G 241 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY G 243 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 256 through 258 Processing sheet with id=AF3, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AF4, first strand: chain 'G' and resid 281 through 282 Processing sheet with id=AF5, first strand: chain 'H' and resid 21 through 25 removed outlier: 7.881A pdb=" N ALA H 58 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU H 40 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY H 60 " --> pdb=" O LEU H 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 79 through 82 removed outlier: 6.455A pdb=" N GLY H 79 " --> pdb=" O SER H 108 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL H 110 " --> pdb=" O GLY H 79 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE H 81 " --> pdb=" O VAL H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'I' and resid 21 through 25 removed outlier: 3.776A pdb=" N ILE I 61 " --> pdb=" O TYR I 76 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU I 38 " --> pdb=" O VAL I 59 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 79 through 82 removed outlier: 6.348A pdb=" N GLY I 79 " --> pdb=" O SER I 108 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL I 110 " --> pdb=" O GLY I 79 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE I 81 " --> pdb=" O VAL I 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'J' and resid 21 through 25 removed outlier: 7.580A pdb=" N ALA J 58 " --> pdb=" O LEU J 40 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU J 40 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY J 60 " --> pdb=" O LEU J 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 78 through 82 removed outlier: 6.737A pdb=" N GLY J 79 " --> pdb=" O SER J 108 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL J 110 " --> pdb=" O GLY J 79 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE J 81 " --> pdb=" O VAL J 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'K' and resid 21 through 25 removed outlier: 3.568A pdb=" N ILE K 61 " --> pdb=" O TYR K 76 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ALA K 58 " --> pdb=" O LEU K 40 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU K 40 " --> pdb=" O ALA K 58 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY K 60 " --> pdb=" O LEU K 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 79 through 82 removed outlier: 6.392A pdb=" N GLY K 79 " --> pdb=" O SER K 108 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL K 110 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE K 81 " --> pdb=" O VAL K 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'L' and resid 21 through 25 removed outlier: 6.737A pdb=" N LEU L 38 " --> pdb=" O VAL L 59 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 79 through 82 removed outlier: 6.552A pdb=" N GLY L 79 " --> pdb=" O SER L 108 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL L 110 " --> pdb=" O GLY L 79 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N PHE L 81 " --> pdb=" O VAL L 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'M' and resid 21 through 25 removed outlier: 7.869A pdb=" N ALA M 58 " --> pdb=" O LEU M 40 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU M 40 " --> pdb=" O ALA M 58 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY M 60 " --> pdb=" O LEU M 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 79 through 82 removed outlier: 6.421A pdb=" N GLY M 79 " --> pdb=" O SER M 108 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL M 110 " --> pdb=" O GLY M 79 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE M 81 " --> pdb=" O VAL M 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'N' and resid 21 through 25 removed outlier: 4.111A pdb=" N GLY N 60 " --> pdb=" O LEU N 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 79 through 82 removed outlier: 6.563A pdb=" N GLY N 79 " --> pdb=" O SER N 108 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL N 110 " --> pdb=" O GLY N 79 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N PHE N 81 " --> pdb=" O VAL N 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 547 hydrogen bonds defined for protein. 1473 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: 4.11 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8053 1.34 - 1.46: 5411 1.46 - 1.58: 11176 1.58 - 1.70: 0 1.70 - 1.82: 203 Bond restraints: 24843 Sorted by residual: bond pdb=" C THR B 74 " pdb=" N PRO B 75 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.55e+00 bond pdb=" CA THR B 74 " pdb=" C THR B 74 " ideal model delta sigma weight residual 1.524 1.545 -0.021 1.26e-02 6.30e+03 2.83e+00 bond pdb=" C TYR D 32 " pdb=" O TYR D 32 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.25e+00 bond pdb=" N GLY B 76 " pdb=" CA GLY B 76 " ideal model delta sigma weight residual 1.446 1.460 -0.014 1.11e-02 8.12e+03 1.59e+00 bond pdb=" N ARG C 66 " pdb=" CA ARG C 66 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.59e+00 ... (remaining 24838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 32671 1.87 - 3.75: 846 3.75 - 5.62: 145 5.62 - 7.50: 30 7.50 - 9.37: 13 Bond angle restraints: 33705 Sorted by residual: angle pdb=" N TRP C 170 " pdb=" CA TRP C 170 " pdb=" C TRP C 170 " ideal model delta sigma weight residual 114.75 107.86 6.89 1.26e+00 6.30e-01 2.99e+01 angle pdb=" N GLY C 67 " pdb=" CA GLY C 67 " pdb=" C GLY C 67 " ideal model delta sigma weight residual 112.29 117.99 -5.70 1.12e+00 7.97e-01 2.59e+01 angle pdb=" N THR E 74 " pdb=" CA THR E 74 " pdb=" C THR E 74 " ideal model delta sigma weight residual 109.81 119.16 -9.35 2.21e+00 2.05e-01 1.79e+01 angle pdb=" N TRP B 170 " pdb=" CA TRP B 170 " pdb=" C TRP B 170 " ideal model delta sigma weight residual 114.75 109.50 5.25 1.26e+00 6.30e-01 1.74e+01 angle pdb=" C SER C 65 " pdb=" N ARG C 66 " pdb=" CA ARG C 66 " ideal model delta sigma weight residual 121.54 129.44 -7.90 1.91e+00 2.74e-01 1.71e+01 ... (remaining 33700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 13541 17.58 - 35.15: 1201 35.15 - 52.73: 217 52.73 - 70.30: 52 70.30 - 87.88: 39 Dihedral angle restraints: 15050 sinusoidal: 5964 harmonic: 9086 Sorted by residual: dihedral pdb=" CA ALA F 51 " pdb=" C ALA F 51 " pdb=" N LEU F 52 " pdb=" CA LEU F 52 " ideal model delta harmonic sigma weight residual -180.00 -115.91 -64.09 0 5.00e+00 4.00e-02 1.64e+02 dihedral pdb=" CA ALA E 51 " pdb=" C ALA E 51 " pdb=" N LEU E 52 " pdb=" CA LEU E 52 " ideal model delta harmonic sigma weight residual 180.00 -117.49 -62.51 0 5.00e+00 4.00e-02 1.56e+02 dihedral pdb=" CA ALA C 51 " pdb=" C ALA C 51 " pdb=" N LEU C 52 " pdb=" CA LEU C 52 " ideal model delta harmonic sigma weight residual -180.00 -119.52 -60.48 0 5.00e+00 4.00e-02 1.46e+02 ... (remaining 15047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2698 0.042 - 0.084: 753 0.084 - 0.126: 268 0.126 - 0.168: 29 0.168 - 0.210: 11 Chirality restraints: 3759 Sorted by residual: chirality pdb=" CA ASP E 313 " pdb=" N ASP E 313 " pdb=" C ASP E 313 " pdb=" CB ASP E 313 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO E 75 " pdb=" N PRO E 75 " pdb=" C PRO E 75 " pdb=" CB PRO E 75 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA PRO G 75 " pdb=" N PRO G 75 " pdb=" C PRO G 75 " pdb=" CB PRO G 75 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3756 not shown) Planarity restraints: 4410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 74 " -0.087 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO B 75 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 201 " 0.055 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO B 202 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 74 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO G 75 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO G 75 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 75 " -0.037 5.00e-02 4.00e+02 ... (remaining 4407 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 595 2.67 - 3.23: 23749 3.23 - 3.79: 35508 3.79 - 4.34: 48274 4.34 - 4.90: 79171 Nonbonded interactions: 187297 Sorted by model distance: nonbonded pdb=" O GLN F 43 " pdb=" OG SER F 69 " model vdw 2.117 3.040 nonbonded pdb=" O GLN D 43 " pdb=" OG SER D 69 " model vdw 2.128 3.040 nonbonded pdb=" O GLN C 43 " pdb=" OG SER C 69 " model vdw 2.134 3.040 nonbonded pdb=" O GLN A 43 " pdb=" OG SER A 69 " model vdw 2.141 3.040 nonbonded pdb=" OE2 GLU A 128 " pdb=" OH TYR A 253 " model vdw 2.156 3.040 ... (remaining 187292 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'H' and (resid 2 through 46 or resid 48 through 110)) selection = (chain 'I' and (resid 2 through 46 or resid 48 through 110)) selection = (chain 'J' and (resid 2 through 46 or resid 48 through 110)) selection = (chain 'K' and (resid 2 through 46 or resid 48 through 110)) selection = (chain 'L' and (resid 2 through 46 or resid 48 through 110)) selection = (chain 'M' and (resid 2 through 46 or resid 48 through 110)) selection = (chain 'N' and (resid 2 through 46 or resid 48 through 110)) } 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=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 32.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 24.450 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 0.064 24843 Z= 0.142 Angle : 0.734 9.369 33705 Z= 0.399 Chirality : 0.045 0.210 3759 Planarity : 0.005 0.136 4410 Dihedral : 14.443 87.879 9212 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.61 % Allowed : 12.36 % Favored : 87.03 % Rotamer: Outliers : 0.27 % Allowed : 0.27 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.61 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.15), residues: 3108 helix: 0.09 (0.24), residues: 543 sheet: -0.97 (0.22), residues: 598 loop : -2.16 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 109 TYR 0.022 0.001 TYR B 53 PHE 0.017 0.001 PHE B 17 TRP 0.026 0.001 TRP G 205 HIS 0.005 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00287 (24843) covalent geometry : angle 0.73358 (33705) hydrogen bonds : bond 0.17446 ( 547) hydrogen bonds : angle 6.70143 ( 1473) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8647 (tm-30) cc_final: 0.7741 (tm-30) REVERT: A 334 GLU cc_start: 0.8336 (tp30) cc_final: 0.8121 (tp30) REVERT: B 145 GLU cc_start: 0.7872 (tp30) cc_final: 0.7642 (tp30) REVERT: B 331 ASP cc_start: 0.6155 (p0) cc_final: 0.5939 (p0) REVERT: C 113 MET cc_start: 0.8092 (mpp) cc_final: 0.7881 (mpp) REVERT: C 129 MET cc_start: 0.8533 (tpp) cc_final: 0.8263 (tpp) REVERT: D 128 GLU cc_start: 0.8207 (tp30) cc_final: 0.7940 (tp30) REVERT: D 153 ASP cc_start: 0.8287 (t0) cc_final: 0.6679 (p0) REVERT: E 3 MET cc_start: 0.6289 (mtm) cc_final: 0.5936 (mtm) REVERT: E 143 THR cc_start: 0.8946 (p) cc_final: 0.8711 (t) REVERT: E 153 ASP cc_start: 0.8557 (t0) cc_final: 0.7995 (t0) REVERT: E 272 MET cc_start: 0.8472 (ptm) cc_final: 0.8183 (ptp) REVERT: F 125 GLN cc_start: 0.7809 (tt0) cc_final: 0.7423 (mt0) REVERT: F 298 ILE cc_start: 0.8018 (tp) cc_final: 0.7809 (tp) REVERT: G 37 GLU cc_start: 0.4205 (pm20) cc_final: 0.3786 (pm20) REVERT: H 41 ASP cc_start: 0.8210 (t0) cc_final: 0.7989 (t0) REVERT: H 44 SER cc_start: 0.8313 (p) cc_final: 0.7854 (p) REVERT: H 53 THR cc_start: 0.9043 (p) cc_final: 0.8678 (p) REVERT: H 72 THR cc_start: 0.9074 (m) cc_final: 0.8775 (p) REVERT: K 39 MET cc_start: 0.7143 (ptm) cc_final: 0.6931 (ptm) REVERT: K 73 LEU cc_start: 0.9032 (mt) cc_final: 0.8791 (mt) REVERT: M 35 MET cc_start: 0.8541 (mpp) cc_final: 0.8215 (mpp) REVERT: M 68 GLN cc_start: 0.8487 (pp30) cc_final: 0.8126 (pp30) REVERT: M 88 TRP cc_start: 0.7090 (m-10) cc_final: 0.6702 (m-10) REVERT: M 98 LYS cc_start: 0.8859 (mtpp) cc_final: 0.8142 (mtpt) outliers start: 0 outliers final: 0 residues processed: 470 average time/residue: 0.1562 time to fit residues: 118.4231 Evaluate side-chains 365 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0070 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0050 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 0.9980 overall best weight: 0.2208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 85 ASN A 160 ASN B 164 GLN D 82 HIS D 270 ASN E 130 GLN E 164 GLN ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 278 GLN I 13 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.086133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.076884 restraints weight = 95065.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.079361 restraints weight = 43572.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.081010 restraints weight = 24929.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.082131 restraints weight = 16191.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.082922 restraints weight = 11413.551| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24843 Z= 0.135 Angle : 0.693 8.899 33705 Z= 0.358 Chirality : 0.045 0.215 3759 Planarity : 0.005 0.114 4410 Dihedral : 6.125 65.624 3423 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.36 % Favored : 87.16 % Rotamer: Outliers : 1.30 % Allowed : 9.61 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.61 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.15), residues: 3108 helix: 0.36 (0.24), residues: 555 sheet: -0.71 (0.22), residues: 595 loop : -2.21 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 99 TYR 0.036 0.001 TYR E 53 PHE 0.014 0.001 PHE C 34 TRP 0.023 0.002 TRP D 308 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00301 (24843) covalent geometry : angle 0.69336 (33705) hydrogen bonds : bond 0.04298 ( 547) hydrogen bonds : angle 5.47374 ( 1473) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 404 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8070 (tt) REVERT: B 331 ASP cc_start: 0.6576 (p0) cc_final: 0.6169 (p0) REVERT: D 50 MET cc_start: 0.5408 (tpt) cc_final: 0.5081 (tpt) REVERT: D 153 ASP cc_start: 0.8317 (t0) cc_final: 0.6876 (p0) REVERT: D 216 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7931 (mt-10) REVERT: E 3 MET cc_start: 0.6300 (mtm) cc_final: 0.5916 (mtm) REVERT: E 272 MET cc_start: 0.8678 (ptm) cc_final: 0.8407 (ptp) REVERT: F 125 GLN cc_start: 0.7677 (tt0) cc_final: 0.7458 (mt0) REVERT: F 331 ASP cc_start: 0.8182 (t0) cc_final: 0.7916 (t0) REVERT: G 326 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.6872 (tt) REVERT: H 15 ASN cc_start: 0.8460 (t0) cc_final: 0.8150 (t0) REVERT: H 41 ASP cc_start: 0.8444 (t0) cc_final: 0.8224 (t0) REVERT: H 44 SER cc_start: 0.8249 (p) cc_final: 0.7806 (p) REVERT: H 72 THR cc_start: 0.9134 (m) cc_final: 0.8835 (p) REVERT: I 4 LYS cc_start: 0.8851 (mmmm) cc_final: 0.8410 (mmmt) REVERT: K 39 MET cc_start: 0.7213 (ptm) cc_final: 0.6817 (ptm) outliers start: 27 outliers final: 16 residues processed: 420 average time/residue: 0.1564 time to fit residues: 105.5631 Evaluate side-chains 369 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 351 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain N residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 297 optimal weight: 0.5980 chunk 274 optimal weight: 0.7980 chunk 211 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 263 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS D 164 GLN ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS G 339 GLN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.072796 restraints weight = 101587.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.075245 restraints weight = 45233.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.076873 restraints weight = 25807.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077984 restraints weight = 16798.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.078732 restraints weight = 11877.231| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24843 Z= 0.220 Angle : 0.740 9.622 33705 Z= 0.384 Chirality : 0.047 0.238 3759 Planarity : 0.006 0.106 4410 Dihedral : 6.361 65.826 3423 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.51 % Favored : 86.00 % Rotamer: Outliers : 2.41 % Allowed : 13.21 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.64 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.15), residues: 3108 helix: 0.36 (0.24), residues: 556 sheet: -1.28 (0.21), residues: 657 loop : -2.19 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 25 TYR 0.020 0.002 TYR E 53 PHE 0.023 0.002 PHE C 34 TRP 0.019 0.002 TRP D 308 HIS 0.016 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00512 (24843) covalent geometry : angle 0.74039 (33705) hydrogen bonds : bond 0.04792 ( 547) hydrogen bonds : angle 5.59766 ( 1473) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 363 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8362 (tt) REVERT: B 145 GLU cc_start: 0.7713 (tp30) cc_final: 0.7476 (tt0) REVERT: B 331 ASP cc_start: 0.7055 (p0) cc_final: 0.6579 (p0) REVERT: C 99 GLN cc_start: 0.8351 (pp30) cc_final: 0.7988 (pp30) REVERT: D 22 LEU cc_start: 0.8549 (tt) cc_final: 0.8340 (tt) REVERT: D 41 LEU cc_start: 0.9043 (tt) cc_final: 0.8791 (mt) REVERT: D 142 MET cc_start: 0.8601 (mtm) cc_final: 0.8331 (mtm) REVERT: D 216 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7853 (mt-10) REVERT: E 82 HIS cc_start: 0.7459 (OUTLIER) cc_final: 0.6996 (m90) REVERT: E 272 MET cc_start: 0.8710 (ptm) cc_final: 0.8302 (ptp) REVERT: F 216 GLU cc_start: 0.8428 (pp20) cc_final: 0.8142 (pp20) REVERT: G 37 GLU cc_start: 0.4354 (pm20) cc_final: 0.3822 (pm20) REVERT: G 326 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7284 (tt) REVERT: H 68 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8543 (mp10) REVERT: H 72 THR cc_start: 0.9149 (m) cc_final: 0.8842 (p) REVERT: I 4 LYS cc_start: 0.8893 (mmmm) cc_final: 0.8622 (mmmt) REVERT: J 102 PHE cc_start: 0.8830 (m-80) cc_final: 0.8629 (m-80) REVERT: K 39 MET cc_start: 0.7212 (ptm) cc_final: 0.6798 (ptm) REVERT: M 35 MET cc_start: 0.8769 (mpp) cc_final: 0.8466 (mpp) REVERT: M 67 ASP cc_start: 0.7875 (t70) cc_final: 0.7572 (t0) REVERT: M 94 ASP cc_start: 0.7542 (p0) cc_final: 0.7322 (p0) REVERT: M 97 LYS cc_start: 0.9126 (ttmm) cc_final: 0.8793 (mtpp) REVERT: N 10 TYR cc_start: 0.8550 (t80) cc_final: 0.8100 (p90) REVERT: N 98 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8314 (mtmm) outliers start: 56 outliers final: 29 residues processed: 396 average time/residue: 0.1482 time to fit residues: 95.6953 Evaluate side-chains 366 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 333 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 41 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 156 optimal weight: 0.0070 chunk 289 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS B 114 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 ASN F 125 GLN G 100 ASN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.070651 restraints weight = 88988.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.072896 restraints weight = 41866.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.074405 restraints weight = 24417.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.075439 restraints weight = 16063.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.076161 restraints weight = 11443.201| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 24843 Z= 0.239 Angle : 0.754 9.767 33705 Z= 0.392 Chirality : 0.048 0.273 3759 Planarity : 0.006 0.101 4410 Dihedral : 6.556 67.052 3423 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.90 % Favored : 85.62 % Rotamer: Outliers : 3.52 % Allowed : 15.24 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.15), residues: 3108 helix: 0.29 (0.24), residues: 556 sheet: -1.29 (0.21), residues: 662 loop : -2.25 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 303 TYR 0.025 0.002 TYR B 53 PHE 0.021 0.002 PHE G 208 TRP 0.016 0.002 TRP I 88 HIS 0.021 0.002 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00556 (24843) covalent geometry : angle 0.75388 (33705) hydrogen bonds : bond 0.04875 ( 547) hydrogen bonds : angle 5.62648 ( 1473) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 358 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8473 (tt) REVERT: B 100 ASN cc_start: 0.8694 (t0) cc_final: 0.8445 (m-40) REVERT: B 128 GLU cc_start: 0.8440 (tp30) cc_final: 0.8063 (tp30) REVERT: B 331 ASP cc_start: 0.7136 (p0) cc_final: 0.6643 (p0) REVERT: C 99 GLN cc_start: 0.8453 (pp30) cc_final: 0.8070 (pp30) REVERT: D 216 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7892 (mt-10) REVERT: E 82 HIS cc_start: 0.7689 (OUTLIER) cc_final: 0.7259 (m90) REVERT: E 145 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7358 (tp30) REVERT: E 272 MET cc_start: 0.8811 (ptm) cc_final: 0.8356 (ptp) REVERT: F 216 GLU cc_start: 0.8442 (pp20) cc_final: 0.8211 (pp20) REVERT: G 37 GLU cc_start: 0.4271 (pm20) cc_final: 0.3828 (pm20) REVERT: G 221 ARG cc_start: 0.4544 (OUTLIER) cc_final: 0.2932 (mpt180) REVERT: G 282 LEU cc_start: 0.8962 (mm) cc_final: 0.8750 (mm) REVERT: G 326 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7832 (tp) REVERT: H 15 ASN cc_start: 0.8705 (t0) cc_final: 0.8471 (t0) REVERT: H 68 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8522 (mp10) REVERT: H 72 THR cc_start: 0.9140 (m) cc_final: 0.8831 (p) REVERT: I 4 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8687 (mmmt) REVERT: K 39 MET cc_start: 0.7186 (ptm) cc_final: 0.6795 (ptm) REVERT: M 35 MET cc_start: 0.8775 (mpp) cc_final: 0.8159 (mpp) REVERT: M 67 ASP cc_start: 0.7842 (t70) cc_final: 0.7610 (t0) REVERT: M 97 LYS cc_start: 0.9155 (ttmm) cc_final: 0.8950 (mtpp) REVERT: N 10 TYR cc_start: 0.8563 (t80) cc_final: 0.8056 (p90) REVERT: N 94 ASP cc_start: 0.7935 (t0) cc_final: 0.7623 (t0) REVERT: N 98 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8319 (mtmm) outliers start: 85 outliers final: 52 residues processed: 419 average time/residue: 0.1454 time to fit residues: 100.2967 Evaluate side-chains 393 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 335 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 193 optimal weight: 0.9980 chunk 267 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 74 optimal weight: 0.3980 chunk 12 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 189 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 ASN G 82 HIS I 13 GLN N 20 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.069457 restraints weight = 124002.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.072047 restraints weight = 52028.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.073776 restraints weight = 28685.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074946 restraints weight = 18283.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.075758 restraints weight = 12783.844| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24843 Z= 0.186 Angle : 0.722 9.492 33705 Z= 0.375 Chirality : 0.046 0.241 3759 Planarity : 0.005 0.119 4410 Dihedral : 6.487 66.468 3423 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.55 % Favored : 86.00 % Rotamer: Outliers : 3.33 % Allowed : 17.04 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.15), residues: 3108 helix: 0.38 (0.24), residues: 555 sheet: -1.18 (0.21), residues: 656 loop : -2.25 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 303 TYR 0.021 0.001 TYR B 53 PHE 0.013 0.001 PHE J 102 TRP 0.021 0.001 TRP F 205 HIS 0.012 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00433 (24843) covalent geometry : angle 0.72235 (33705) hydrogen bonds : bond 0.04541 ( 547) hydrogen bonds : angle 5.49960 ( 1473) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 355 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8348 (tt) REVERT: B 17 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6750 (m-10) REVERT: B 100 ASN cc_start: 0.8644 (t0) cc_final: 0.8386 (m-40) REVERT: B 128 GLU cc_start: 0.8371 (tp30) cc_final: 0.7978 (tp30) REVERT: B 331 ASP cc_start: 0.7232 (p0) cc_final: 0.6724 (p0) REVERT: C 37 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.5305 (mm-30) REVERT: C 99 GLN cc_start: 0.8514 (pp30) cc_final: 0.8130 (pp30) REVERT: C 113 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8145 (mpp) REVERT: D 216 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7921 (mt-10) REVERT: E 82 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.7319 (m90) REVERT: E 145 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: E 272 MET cc_start: 0.8812 (ptm) cc_final: 0.8403 (ptp) REVERT: F 70 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8214 (p) REVERT: F 331 ASP cc_start: 0.8295 (t0) cc_final: 0.8053 (t0) REVERT: G 221 ARG cc_start: 0.4515 (OUTLIER) cc_final: 0.2910 (mpt180) REVERT: G 326 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7740 (tp) REVERT: H 15 ASN cc_start: 0.8775 (t0) cc_final: 0.8515 (t0) REVERT: H 72 THR cc_start: 0.9161 (m) cc_final: 0.8859 (p) REVERT: I 4 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8671 (mmmt) REVERT: K 39 MET cc_start: 0.7172 (ptm) cc_final: 0.6733 (ptm) REVERT: K 62 LEU cc_start: 0.9385 (tp) cc_final: 0.9163 (mp) REVERT: K 68 GLN cc_start: 0.9123 (mp-120) cc_final: 0.8833 (mm-40) REVERT: M 35 MET cc_start: 0.8842 (mpp) cc_final: 0.8229 (mpp) REVERT: M 94 ASP cc_start: 0.7685 (p0) cc_final: 0.7429 (p0) REVERT: M 97 LYS cc_start: 0.9145 (ttmm) cc_final: 0.8833 (mtpp) REVERT: N 10 TYR cc_start: 0.8603 (t80) cc_final: 0.7860 (p90) REVERT: N 94 ASP cc_start: 0.7859 (t0) cc_final: 0.7533 (t0) REVERT: N 98 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8287 (mtmm) outliers start: 80 outliers final: 52 residues processed: 410 average time/residue: 0.1472 time to fit residues: 98.4677 Evaluate side-chains 397 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 336 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 34 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 289 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 299 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.081487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.072254 restraints weight = 102887.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074703 restraints weight = 46169.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.076333 restraints weight = 26328.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077427 restraints weight = 17098.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078199 restraints weight = 12095.005| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24843 Z= 0.191 Angle : 0.731 9.509 33705 Z= 0.379 Chirality : 0.047 0.254 3759 Planarity : 0.005 0.125 4410 Dihedral : 6.481 66.062 3423 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.87 % Favored : 85.68 % Rotamer: Outliers : 3.75 % Allowed : 17.89 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.15), residues: 3108 helix: 0.32 (0.24), residues: 556 sheet: -1.26 (0.21), residues: 671 loop : -2.21 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 303 TYR 0.023 0.001 TYR F 140 PHE 0.026 0.001 PHE G 208 TRP 0.021 0.001 TRP M 88 HIS 0.008 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00445 (24843) covalent geometry : angle 0.73082 (33705) hydrogen bonds : bond 0.04512 ( 547) hydrogen bonds : angle 5.51078 ( 1473) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 353 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8136 (mmm) cc_final: 0.7752 (mmm) REVERT: A 326 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8278 (tt) REVERT: B 17 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6714 (m-10) REVERT: B 100 ASN cc_start: 0.8593 (t0) cc_final: 0.8367 (m-40) REVERT: B 128 GLU cc_start: 0.8310 (tp30) cc_final: 0.7937 (tp30) REVERT: B 331 ASP cc_start: 0.7223 (p0) cc_final: 0.6736 (p0) REVERT: C 37 GLU cc_start: 0.5775 (OUTLIER) cc_final: 0.5060 (mm-30) REVERT: C 99 GLN cc_start: 0.8449 (pp30) cc_final: 0.8083 (pp30) REVERT: C 159 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8251 (mm-30) REVERT: D 3 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7963 (ttp) REVERT: D 128 GLU cc_start: 0.7965 (tp30) cc_final: 0.7696 (tp30) REVERT: D 216 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7827 (mt-10) REVERT: E 82 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7250 (m90) REVERT: E 145 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7301 (tp30) REVERT: E 272 MET cc_start: 0.8700 (ptm) cc_final: 0.8243 (ptp) REVERT: F 70 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8178 (p) REVERT: F 331 ASP cc_start: 0.8268 (t0) cc_final: 0.8048 (t0) REVERT: G 100 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8313 (p0) REVERT: G 221 ARG cc_start: 0.4626 (OUTLIER) cc_final: 0.2981 (mpt180) REVERT: G 326 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7747 (tp) REVERT: H 15 ASN cc_start: 0.8706 (t0) cc_final: 0.8506 (t0) REVERT: H 72 THR cc_start: 0.9119 (m) cc_final: 0.8818 (p) REVERT: I 4 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8666 (mmmt) REVERT: K 39 MET cc_start: 0.7161 (ptm) cc_final: 0.6795 (ptm) REVERT: M 35 MET cc_start: 0.8740 (mpp) cc_final: 0.8152 (mpp) REVERT: M 94 ASP cc_start: 0.7587 (p0) cc_final: 0.7274 (p0) REVERT: M 97 LYS cc_start: 0.9144 (ttmm) cc_final: 0.8925 (mtpp) REVERT: N 10 TYR cc_start: 0.8558 (t80) cc_final: 0.7848 (p90) REVERT: N 94 ASP cc_start: 0.7822 (t0) cc_final: 0.7504 (t0) REVERT: N 98 LYS cc_start: 0.8566 (mtmm) cc_final: 0.8291 (mtmm) outliers start: 91 outliers final: 59 residues processed: 419 average time/residue: 0.1488 time to fit residues: 102.7413 Evaluate side-chains 404 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 335 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 223 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 289 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 271 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 238 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.079281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.070065 restraints weight = 102068.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.072464 restraints weight = 46169.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074061 restraints weight = 26445.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.075152 restraints weight = 17286.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.075904 restraints weight = 12263.330| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 24843 Z= 0.220 Angle : 0.751 9.750 33705 Z= 0.390 Chirality : 0.047 0.267 3759 Planarity : 0.005 0.130 4410 Dihedral : 6.546 65.642 3423 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.45 % Allowed : 14.35 % Favored : 85.20 % Rotamer: Outliers : 3.94 % Allowed : 18.73 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.61 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.15), residues: 3108 helix: 0.27 (0.24), residues: 556 sheet: -1.51 (0.20), residues: 749 loop : -2.25 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 303 TYR 0.021 0.001 TYR F 140 PHE 0.022 0.001 PHE G 208 TRP 0.031 0.002 TRP M 88 HIS 0.012 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00513 (24843) covalent geometry : angle 0.75053 (33705) hydrogen bonds : bond 0.04648 ( 547) hydrogen bonds : angle 5.59018 ( 1473) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 339 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8233 (mmm) cc_final: 0.7867 (mmm) REVERT: A 326 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8311 (tt) REVERT: B 100 ASN cc_start: 0.8626 (t0) cc_final: 0.8367 (m-40) REVERT: B 128 GLU cc_start: 0.8355 (tp30) cc_final: 0.7966 (tp30) REVERT: B 331 ASP cc_start: 0.7309 (p0) cc_final: 0.6790 (p0) REVERT: C 37 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5140 (mm-30) REVERT: C 83 GLU cc_start: 0.8050 (tp30) cc_final: 0.7345 (tt0) REVERT: C 113 MET cc_start: 0.8172 (mpp) cc_final: 0.7916 (mpp) REVERT: C 159 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8298 (mm-30) REVERT: D 3 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8016 (ttp) REVERT: D 128 GLU cc_start: 0.8046 (tp30) cc_final: 0.7765 (tp30) REVERT: D 140 TYR cc_start: 0.6312 (t80) cc_final: 0.5981 (t80) REVERT: D 216 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7891 (mt-10) REVERT: E 82 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7270 (m90) REVERT: E 145 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: E 250 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.9291 (mm) REVERT: E 272 MET cc_start: 0.8751 (ptm) cc_final: 0.8315 (ptp) REVERT: F 70 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8174 (p) REVERT: F 216 GLU cc_start: 0.8460 (pp20) cc_final: 0.8167 (pp20) REVERT: G 221 ARG cc_start: 0.4615 (OUTLIER) cc_final: 0.2946 (mpt180) REVERT: G 326 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7862 (tp) REVERT: H 72 THR cc_start: 0.9147 (m) cc_final: 0.8844 (p) REVERT: I 4 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8679 (mmmt) REVERT: K 39 MET cc_start: 0.7178 (ptm) cc_final: 0.6762 (ptm) REVERT: M 35 MET cc_start: 0.8796 (mpp) cc_final: 0.8124 (mpp) REVERT: M 94 ASP cc_start: 0.7647 (p0) cc_final: 0.7402 (p0) REVERT: N 10 TYR cc_start: 0.8574 (t80) cc_final: 0.8028 (p90) REVERT: N 94 ASP cc_start: 0.7969 (t0) cc_final: 0.7637 (t0) REVERT: N 98 LYS cc_start: 0.8603 (mtmm) cc_final: 0.8315 (mtmm) outliers start: 96 outliers final: 65 residues processed: 405 average time/residue: 0.1451 time to fit residues: 97.9078 Evaluate side-chains 407 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 333 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 34 PHE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 39 MET Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 189 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 0.0040 chunk 205 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 251 optimal weight: 0.0030 chunk 181 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 293 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.080973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070952 restraints weight = 130482.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.073643 restraints weight = 53932.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.075429 restraints weight = 29655.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.076626 restraints weight = 18873.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.077457 restraints weight = 13178.891| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24843 Z= 0.167 Angle : 0.731 10.227 33705 Z= 0.376 Chirality : 0.046 0.279 3759 Planarity : 0.005 0.133 4410 Dihedral : 6.423 66.018 3423 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.03 % Favored : 86.55 % Rotamer: Outliers : 3.60 % Allowed : 19.34 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.15), residues: 3108 helix: 0.41 (0.24), residues: 555 sheet: -1.36 (0.21), residues: 699 loop : -2.16 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 45 TYR 0.020 0.001 TYR B 53 PHE 0.019 0.001 PHE G 208 TRP 0.023 0.001 TRP M 88 HIS 0.007 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00387 (24843) covalent geometry : angle 0.73069 (33705) hydrogen bonds : bond 0.04293 ( 547) hydrogen bonds : angle 5.41148 ( 1473) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 350 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8188 (mmm) cc_final: 0.7867 (mmm) REVERT: A 326 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8221 (tt) REVERT: B 100 ASN cc_start: 0.8605 (t0) cc_final: 0.8369 (m-40) REVERT: B 128 GLU cc_start: 0.8297 (tp30) cc_final: 0.7938 (tp30) REVERT: B 331 ASP cc_start: 0.7255 (p0) cc_final: 0.6753 (p0) REVERT: C 37 GLU cc_start: 0.5752 (OUTLIER) cc_final: 0.5117 (mm-30) REVERT: C 99 GLN cc_start: 0.8585 (pp30) cc_final: 0.8087 (pp30) REVERT: C 159 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8288 (mm-30) REVERT: D 3 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.8011 (ttp) REVERT: D 216 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7897 (mt-10) REVERT: E 82 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7200 (m90) REVERT: E 145 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7266 (tp30) REVERT: E 259 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7948 (mm-30) REVERT: E 272 MET cc_start: 0.8696 (ptm) cc_final: 0.8277 (ptp) REVERT: F 43 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7821 (pp30) REVERT: F 70 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8110 (p) REVERT: F 159 GLU cc_start: 0.8384 (tp30) cc_final: 0.8128 (tp30) REVERT: F 216 GLU cc_start: 0.8339 (pp20) cc_final: 0.8090 (pp20) REVERT: G 82 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.7640 (t-90) REVERT: G 100 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8407 (p0) REVERT: G 326 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7452 (tt) REVERT: H 72 THR cc_start: 0.9129 (m) cc_final: 0.8821 (p) REVERT: I 4 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8670 (mmmt) REVERT: K 31 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7676 (mmtm) REVERT: K 39 MET cc_start: 0.7048 (ptm) cc_final: 0.6633 (ptm) REVERT: L 4 LYS cc_start: 0.4304 (mmtm) cc_final: 0.3967 (tptp) REVERT: M 35 MET cc_start: 0.8799 (mpp) cc_final: 0.8208 (mpp) REVERT: N 10 TYR cc_start: 0.8575 (t80) cc_final: 0.7853 (p90) REVERT: N 94 ASP cc_start: 0.7929 (t0) cc_final: 0.7601 (t0) REVERT: N 98 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8268 (mtmm) outliers start: 87 outliers final: 59 residues processed: 410 average time/residue: 0.1472 time to fit residues: 99.6601 Evaluate side-chains 405 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 336 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 170 TRP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 34 PHE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 100 ASN Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 179 optimal weight: 0.0370 chunk 18 optimal weight: 0.9980 chunk 272 optimal weight: 0.0010 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 overall best weight: 0.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.071920 restraints weight = 100671.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.074330 restraints weight = 45402.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.075943 restraints weight = 26134.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.077030 restraints weight = 17089.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.077787 restraints weight = 12137.179| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24843 Z= 0.166 Angle : 0.730 10.127 33705 Z= 0.377 Chirality : 0.046 0.277 3759 Planarity : 0.005 0.128 4410 Dihedral : 6.376 65.589 3423 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.74 % Favored : 85.81 % Rotamer: Outliers : 3.37 % Allowed : 19.88 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.15), residues: 3108 helix: 0.42 (0.24), residues: 555 sheet: -1.29 (0.21), residues: 699 loop : -2.15 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 45 TYR 0.023 0.001 TYR E 106 PHE 0.025 0.001 PHE G 208 TRP 0.036 0.001 TRP G 205 HIS 0.002 0.001 HIS N 20 Details of bonding type rmsd covalent geometry : bond 0.00388 (24843) covalent geometry : angle 0.73043 (33705) hydrogen bonds : bond 0.04225 ( 547) hydrogen bonds : angle 5.39510 ( 1473) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 337 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8196 (mmm) cc_final: 0.7889 (mmm) REVERT: A 326 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8227 (tt) REVERT: B 100 ASN cc_start: 0.8607 (t0) cc_final: 0.8379 (m-40) REVERT: B 128 GLU cc_start: 0.8288 (tp30) cc_final: 0.7925 (tp30) REVERT: B 331 ASP cc_start: 0.7265 (p0) cc_final: 0.6761 (p0) REVERT: C 37 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.5161 (mm-30) REVERT: C 99 GLN cc_start: 0.8570 (pp30) cc_final: 0.8088 (pp30) REVERT: C 159 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8291 (mm-30) REVERT: D 3 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8006 (ttp) REVERT: D 216 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7895 (mt-10) REVERT: E 82 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7142 (m90) REVERT: E 272 MET cc_start: 0.8718 (ptm) cc_final: 0.8275 (ptp) REVERT: F 43 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7849 (pp30) REVERT: F 70 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8122 (p) REVERT: F 159 GLU cc_start: 0.8344 (tp30) cc_final: 0.8101 (tp30) REVERT: F 216 GLU cc_start: 0.8314 (pp20) cc_final: 0.8067 (pp20) REVERT: G 3 MET cc_start: 0.7795 (pmm) cc_final: 0.7293 (pmm) REVERT: G 77 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.8166 (t80) REVERT: G 82 HIS cc_start: 0.8508 (OUTLIER) cc_final: 0.7788 (t-90) REVERT: G 221 ARG cc_start: 0.4463 (OUTLIER) cc_final: 0.2844 (mpt180) REVERT: G 326 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7416 (tt) REVERT: H 72 THR cc_start: 0.9122 (m) cc_final: 0.8809 (p) REVERT: I 4 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8666 (mmmt) REVERT: K 39 MET cc_start: 0.7075 (ptm) cc_final: 0.6632 (ptm) REVERT: L 4 LYS cc_start: 0.4189 (mmtm) cc_final: 0.3917 (tptp) REVERT: M 35 MET cc_start: 0.8802 (mpp) cc_final: 0.8304 (mpp) REVERT: N 10 TYR cc_start: 0.8568 (t80) cc_final: 0.7849 (p90) REVERT: N 94 ASP cc_start: 0.7950 (t0) cc_final: 0.7643 (t0) REVERT: N 98 LYS cc_start: 0.8584 (mtmm) cc_final: 0.8341 (mtmm) outliers start: 81 outliers final: 63 residues processed: 397 average time/residue: 0.1482 time to fit residues: 97.3572 Evaluate side-chains 401 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 328 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 170 TRP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 34 PHE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 170 TRP Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 90 optimal weight: 0.0770 chunk 103 optimal weight: 0.4980 chunk 46 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 276 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.082009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.072787 restraints weight = 98074.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.075214 restraints weight = 44380.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076822 restraints weight = 25521.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077922 restraints weight = 16688.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.078655 restraints weight = 11840.406| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24843 Z= 0.158 Angle : 0.739 10.675 33705 Z= 0.379 Chirality : 0.047 0.299 3759 Planarity : 0.005 0.138 4410 Dihedral : 6.319 65.384 3423 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.42 % Favored : 86.16 % Rotamer: Outliers : 3.45 % Allowed : 20.11 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.15), residues: 3108 helix: 0.46 (0.24), residues: 554 sheet: -1.07 (0.21), residues: 675 loop : -2.21 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 45 TYR 0.019 0.001 TYR E 53 PHE 0.026 0.001 PHE G 208 TRP 0.065 0.002 TRP G 205 HIS 0.003 0.001 HIS J 20 Details of bonding type rmsd covalent geometry : bond 0.00367 (24843) covalent geometry : angle 0.73866 (33705) hydrogen bonds : bond 0.04117 ( 547) hydrogen bonds : angle 5.31449 ( 1473) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 338 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8187 (mmm) cc_final: 0.7870 (mmm) REVERT: A 326 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8186 (tt) REVERT: B 100 ASN cc_start: 0.8616 (t0) cc_final: 0.8383 (m-40) REVERT: B 128 GLU cc_start: 0.8309 (tp30) cc_final: 0.7976 (tp30) REVERT: B 331 ASP cc_start: 0.7257 (p0) cc_final: 0.6739 (p0) REVERT: C 37 GLU cc_start: 0.5674 (OUTLIER) cc_final: 0.5136 (mm-30) REVERT: C 99 GLN cc_start: 0.8564 (pp30) cc_final: 0.8095 (pp30) REVERT: C 142 MET cc_start: 0.8273 (mtp) cc_final: 0.7937 (mmm) REVERT: D 3 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8026 (ttp) REVERT: D 139 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8820 (mmmm) REVERT: D 216 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7830 (mt-10) REVERT: E 82 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7118 (m90) REVERT: E 259 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8222 (mm-30) REVERT: E 272 MET cc_start: 0.8701 (ptm) cc_final: 0.8302 (ptp) REVERT: F 43 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7900 (pp30) REVERT: F 70 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8095 (p) REVERT: F 159 GLU cc_start: 0.8348 (tp30) cc_final: 0.8125 (tp30) REVERT: F 216 GLU cc_start: 0.8306 (pp20) cc_final: 0.8057 (pp20) REVERT: G 3 MET cc_start: 0.7721 (pmm) cc_final: 0.7480 (pmm) REVERT: G 77 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.8032 (t80) REVERT: G 82 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.7738 (t-90) REVERT: G 221 ARG cc_start: 0.4451 (OUTLIER) cc_final: 0.2831 (mpt180) REVERT: G 326 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7537 (tp) REVERT: H 72 THR cc_start: 0.9105 (m) cc_final: 0.8795 (p) REVERT: I 4 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8665 (mmmt) REVERT: K 39 MET cc_start: 0.7159 (ptm) cc_final: 0.6624 (ptm) REVERT: L 4 LYS cc_start: 0.4193 (mmtm) cc_final: 0.3972 (tptp) REVERT: M 35 MET cc_start: 0.8803 (mpp) cc_final: 0.8341 (mpp) REVERT: N 10 TYR cc_start: 0.8563 (t80) cc_final: 0.7858 (p90) REVERT: N 94 ASP cc_start: 0.7947 (t0) cc_final: 0.7626 (t0) REVERT: N 98 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8327 (mtmm) outliers start: 83 outliers final: 63 residues processed: 397 average time/residue: 0.1491 time to fit residues: 97.3960 Evaluate side-chains 404 residues out of total 2597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 330 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 205 TRP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 170 TRP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain G residue 34 PHE Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 170 TRP Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain J residue 108 SER Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 296 optimal weight: 3.9990 chunk 287 optimal weight: 0.0970 chunk 50 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 240 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 12 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.081914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.072444 restraints weight = 106756.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074958 restraints weight = 47081.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076620 restraints weight = 26654.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.077743 restraints weight = 17265.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078533 restraints weight = 12196.265| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24843 Z= 0.174 Angle : 0.852 59.197 33705 Z= 0.456 Chirality : 0.047 0.590 3759 Planarity : 0.005 0.136 4410 Dihedral : 6.344 65.323 3423 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.42 % Favored : 86.13 % Rotamer: Outliers : 3.33 % Allowed : 20.07 % Favored : 76.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.15), residues: 3108 helix: 0.45 (0.24), residues: 555 sheet: -1.07 (0.21), residues: 675 loop : -2.20 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 303 TYR 0.019 0.001 TYR E 53 PHE 0.024 0.001 PHE G 208 TRP 0.052 0.002 TRP G 205 HIS 0.003 0.001 HIS J 20 Details of bonding type rmsd covalent geometry : bond 0.00395 (24843) covalent geometry : angle 0.85183 (33705) hydrogen bonds : bond 0.04126 ( 547) hydrogen bonds : angle 5.31875 ( 1473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4732.49 seconds wall clock time: 82 minutes 40.05 seconds (4960.05 seconds total)