Starting phenix.real_space_refine on Fri Aug 7 05:56:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9crq_45875/08_2026/9crq_45875.cif Found real_map, /net/cci-nas-00/data/ceres_data/9crq_45875/08_2026/9crq_45875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9crq_45875/08_2026/9crq_45875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9crq_45875/08_2026/9crq_45875.map" model { file = "/net/cci-nas-00/data/ceres_data/9crq_45875/08_2026/9crq_45875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9crq_45875/08_2026/9crq_45875.cif" } resolution = 3.07 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 459 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 52 5.49 5 S 57 5.16 5 C 11919 2.51 5 N 3182 2.21 5 O 3764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18974 Number of models: 1 Model: "" Number of chains: 17 Chain: "M" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 373 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "S" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 740 Classifications: {'RNA': 35} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 11, 'rna3p_pur': 11, 'rna3p_pyr': 6} Link IDs: {'rna2p': 18, 'rna3p': 16} Chain: "B" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "C" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "A" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "G" Number of atoms: 1692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1687 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 211, 1687 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 bond proxies already assigned to first conformer: 1722 Chain: "E" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2337 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain breaks: 1 Chain: "K" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Chain: "L" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain breaks: 1 Chain: "H" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Chain: "N" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Chain: "S" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.93, per 1000 atoms: 0.26 Number of scatterers: 18974 At special positions: 0 Unit cell: (110.76, 120.7, 171.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 52 15.00 O 3764 8.00 N 3182 7.00 C 11919 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 901.6 milliseconds 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4242 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 25 sheets defined 41.7% alpha, 16.6% beta 15 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'B' and resid 49 through 69 removed outlier: 4.292A pdb=" N LEU B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.926A pdb=" N GLN B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.555A pdb=" N LEU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.549A pdb=" N ASP B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 195 removed outlier: 3.635A pdb=" N ILE B 195 " --> pdb=" O GLU B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 195' Processing helix chain 'B' and resid 207 through 225 removed outlier: 3.638A pdb=" N LEU B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 4.310A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.548A pdb=" N ASN B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 320 removed outlier: 4.064A pdb=" N LEU B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 69 removed outlier: 4.289A pdb=" N LEU C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.927A pdb=" N GLN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.552A pdb=" N LEU C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 113 Processing helix chain 'C' and resid 115 through 122 removed outlier: 3.551A pdb=" N ASP C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 195 removed outlier: 3.635A pdb=" N ILE C 195 " --> pdb=" O GLU C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 192 through 195' Processing helix chain 'C' and resid 207 through 225 removed outlier: 3.637A pdb=" N LEU C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ALA C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 4.310A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.547A pdb=" N ASN C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 320 removed outlier: 4.062A pdb=" N LEU C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 69 removed outlier: 4.291A pdb=" N LEU D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 78 removed outlier: 3.926A pdb=" N GLN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.552A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.550A pdb=" N ASP D 119 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 195 removed outlier: 3.634A pdb=" N ILE D 195 " --> pdb=" O GLU D 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 192 through 195' Processing helix chain 'D' and resid 207 through 225 removed outlier: 3.637A pdb=" N LEU D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ALA D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 removed outlier: 4.311A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 285 removed outlier: 3.548A pdb=" N ASN D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 removed outlier: 4.064A pdb=" N LEU D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 69 removed outlier: 4.398A pdb=" N LEU A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.742A pdb=" N GLN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.567A pdb=" N ILE A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.678A pdb=" N ASP A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 225 removed outlier: 3.822A pdb=" N LEU A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYS A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 4.077A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.771A pdb=" N THR A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 320 removed outlier: 4.056A pdb=" N LEU A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 42 Processing helix chain 'G' and resid 129 through 138 Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.743A pdb=" N ILE G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 69 removed outlier: 4.161A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 removed outlier: 3.820A pdb=" N GLN E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 103 through 115 Processing helix chain 'E' and resid 115 through 121 removed outlier: 3.501A pdb=" N ASP E 119 " --> pdb=" O ASP E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 232 removed outlier: 3.559A pdb=" N LEU E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYS E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER E 228 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 284 removed outlier: 3.525A pdb=" N THR E 273 " --> pdb=" O TYR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 320 removed outlier: 3.769A pdb=" N LEU E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 26 Processing helix chain 'K' and resid 28 through 36 Processing helix chain 'K' and resid 39 through 60 Processing helix chain 'K' and resid 102 through 116 Processing helix chain 'K' and resid 117 through 144 removed outlier: 3.719A pdb=" N ARG K 121 " --> pdb=" O VAL K 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 26 Processing helix chain 'L' and resid 28 through 36 Processing helix chain 'L' and resid 39 through 60 Processing helix chain 'L' and resid 102 through 116 Processing helix chain 'L' and resid 117 through 145 removed outlier: 3.717A pdb=" N ARG L 121 " --> pdb=" O VAL L 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 26 Processing helix chain 'H' and resid 28 through 36 Processing helix chain 'H' and resid 39 through 60 Processing helix chain 'H' and resid 102 through 116 Processing helix chain 'H' and resid 117 through 144 removed outlier: 3.723A pdb=" N ARG H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 26 Processing helix chain 'N' and resid 28 through 37 Processing helix chain 'N' and resid 39 through 60 Processing helix chain 'N' and resid 102 through 116 Processing helix chain 'N' and resid 117 through 137 removed outlier: 3.661A pdb=" N ARG N 121 " --> pdb=" O VAL N 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2 through 13 current: chain 'B' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 174 through 190 current: chain 'B' and resid 289 through 295 removed outlier: 4.363A pdb=" N THR B 306 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 125 Processing sheet with id=AA4, first strand: chain 'C' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 2 through 13 current: chain 'C' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 174 through 190 current: chain 'C' and resid 289 through 295 removed outlier: 4.362A pdb=" N THR C 306 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 36 Processing sheet with id=AA6, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AA7, first strand: chain 'D' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 2 through 13 current: chain 'D' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 174 through 190 current: chain 'D' and resid 289 through 295 removed outlier: 4.360A pdb=" N THR D 306 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 29 through 36 Processing sheet with id=AA9, first strand: chain 'D' and resid 123 through 125 Processing sheet with id=AB1, first strand: chain 'A' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2 through 13 current: chain 'A' and resid 174 through 182 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 174 through 182 current: chain 'A' and resid 289 through 295 removed outlier: 3.699A pdb=" N THR A 306 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AB3, first strand: chain 'A' and resid 124 through 125 removed outlier: 3.573A pdb=" N VAL A 131 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 68 through 73 removed outlier: 3.838A pdb=" N ASN G 154 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS G 9 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL G 152 " --> pdb=" O LYS G 9 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 13 through 14 removed outlier: 3.643A pdb=" N PHE G 14 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 161 through 163 removed outlier: 3.736A pdb=" N LYS G 161 " --> pdb=" O GLU G 231 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER G 240 " --> pdb=" O GLU G 228 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR G 230 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL G 238 " --> pdb=" O TYR G 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AB8, first strand: chain 'G' and resid 173 through 174 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 173 through 174 current: chain 'G' and resid 205 through 213 removed outlier: 3.506A pdb=" N THR G 213 " --> pdb=" O ALA G 218 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA G 218 " --> pdb=" O THR G 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 2 through 13 current: chain 'E' and resid 178 through 190 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 178 through 190 current: chain 'E' and resid 289 through 295 removed outlier: 4.195A pdb=" N THR E 306 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 17 through 21 removed outlier: 4.293A pdb=" N LYS E 26 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N SER E 20 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU E 24 " --> pdb=" O SER E 20 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 29 through 36 Processing sheet with id=AC3, first strand: chain 'E' and resid 123 through 125 Processing sheet with id=AC4, first strand: chain 'K' and resid 63 through 69 Processing sheet with id=AC5, first strand: chain 'L' and resid 63 through 69 Processing sheet with id=AC6, first strand: chain 'H' and resid 63 through 69 Processing sheet with id=AC7, first strand: chain 'N' and resid 63 through 68 759 hydrogen bonds defined for protein. 2202 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5242 1.33 - 1.46: 4266 1.46 - 1.58: 9664 1.58 - 1.71: 103 1.71 - 1.83: 111 Bond restraints: 19386 Sorted by residual: bond pdb=" C3' DG M 7 " pdb=" C2' DG M 7 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.38e+01 bond pdb=" CZ ARG K 121 " pdb=" NH2 ARG K 121 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.52e+00 bond pdb=" CZ ARG N 52 " pdb=" NH2 ARG N 52 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.64e+00 bond pdb=" CZ ARG L 133 " pdb=" NH2 ARG L 133 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.59e+00 bond pdb=" C3' DC M 10 " pdb=" C2' DC M 10 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.41e+00 ... (remaining 19381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 24172 1.35 - 2.69: 1785 2.69 - 4.04: 401 4.04 - 5.38: 41 5.38 - 6.73: 4 Bond angle restraints: 26403 Sorted by residual: angle pdb=" C ASN E 11 " pdb=" N LEU E 12 " pdb=" CA LEU E 12 " ideal model delta sigma weight residual 122.93 129.66 -6.73 1.51e+00 4.39e-01 1.99e+01 angle pdb=" N3 DT M 17 " pdb=" C4 DT M 17 " pdb=" O4 DT M 17 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT M 15 " pdb=" C4 DT M 15 " pdb=" O4 DT M 15 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT M 16 " pdb=" C4 DT M 16 " pdb=" O4 DT M 16 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT M 14 " pdb=" C4 DT M 14 " pdb=" O4 DT M 14 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 26398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 11437 33.64 - 67.28: 291 67.28 - 100.92: 28 100.92 - 134.55: 0 134.55 - 168.19: 2 Dihedral angle restraints: 11758 sinusoidal: 5141 harmonic: 6617 Sorted by residual: dihedral pdb=" O4' U S 32 " pdb=" C1' U S 32 " pdb=" N1 U S 32 " pdb=" C2 U S 32 " ideal model delta sinusoidal sigma weight residual 232.00 135.36 96.64 1 1.70e+01 3.46e-03 3.71e+01 dihedral pdb=" O4' U S 2 " pdb=" C1' U S 2 " pdb=" N1 U S 2 " pdb=" C2 U S 2 " ideal model delta sinusoidal sigma weight residual -128.00 -45.43 -82.57 1 1.70e+01 3.46e-03 2.89e+01 dihedral pdb=" C4' DG M 13 " pdb=" C3' DG M 13 " pdb=" O3' DG M 13 " pdb=" P DT M 14 " ideal model delta sinusoidal sigma weight residual 220.00 51.81 168.19 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 11755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2600 0.075 - 0.149: 444 0.149 - 0.224: 13 0.224 - 0.299: 7 0.299 - 0.373: 1 Chirality restraints: 3065 Sorted by residual: chirality pdb=" CB VAL E 18 " pdb=" CA VAL E 18 " pdb=" CG1 VAL E 18 " pdb=" CG2 VAL E 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA GLU L 26 " pdb=" N GLU L 26 " pdb=" C GLU L 26 " pdb=" CB GLU L 26 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA GLU H 26 " pdb=" N GLU H 26 " pdb=" C GLU H 26 " pdb=" CB GLU H 26 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 3062 not shown) Planarity restraints: 3163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 48 " -0.107 2.00e-02 2.50e+03 5.64e-02 6.37e+01 pdb=" CG TYR N 48 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR N 48 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR N 48 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR N 48 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR N 48 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR N 48 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR N 48 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 48 " -0.107 2.00e-02 2.50e+03 5.64e-02 6.36e+01 pdb=" CG TYR L 48 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR L 48 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR L 48 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR L 48 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR L 48 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR L 48 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 48 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 48 " -0.106 2.00e-02 2.50e+03 5.58e-02 6.23e+01 pdb=" CG TYR H 48 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR H 48 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR H 48 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR H 48 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR H 48 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR H 48 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 48 " -0.080 2.00e-02 2.50e+03 ... (remaining 3160 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 9 2.20 - 2.88: 6456 2.88 - 3.55: 25011 3.55 - 4.23: 39545 4.23 - 4.90: 72269 Nonbonded interactions: 143290 Sorted by model distance: nonbonded pdb=" CG MET H 128 " pdb=" CB SER N 103 " model vdw 1.527 3.840 nonbonded pdb=" CB MET H 128 " pdb=" CB SER N 103 " model vdw 1.869 3.840 nonbonded pdb=" CB ALA H 125 " pdb=" OE1 GLN N 104 " model vdw 2.021 3.460 nonbonded pdb=" NE2 GLN K 55 " pdb=" OD2 ASP K 59 " model vdw 2.072 3.120 nonbonded pdb=" NE2 GLN L 55 " pdb=" OD2 ASP L 59 " model vdw 2.076 3.120 ... (remaining 143285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 158 or resid 176 through 320)) selection = (chain 'B' and (resid 1 through 158 or resid 176 through 320)) selection = (chain 'C' and (resid 1 through 158 or resid 176 through 320)) selection = (chain 'D' and (resid 1 through 158 or resid 176 through 320)) selection = (chain 'E' and resid 1 through 320) } ncs_group { reference = (chain 'H' and (resid 6 through 68 or resid 80 through 137)) selection = (chain 'K' and (resid 6 through 68 or resid 80 through 137)) selection = (chain 'L' and (resid 6 through 68 or resid 80 through 137)) selection = (chain 'N' and resid 6 through 137) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.120 Find NCS groups from input model: 0.420 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 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 : 0.006 0.040 19386 Z= 0.350 Angle : 0.777 6.731 26403 Z= 0.523 Chirality : 0.052 0.373 3065 Planarity : 0.006 0.078 3163 Dihedral : 14.766 168.194 7516 Min Nonbonded Distance : 1.527 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.31 % Allowed : 0.46 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.17), residues: 2254 helix: 1.59 (0.17), residues: 893 sheet: 1.22 (0.23), residues: 465 loop : -1.03 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 13 TYR 0.107 0.005 TYR N 48 PHE 0.027 0.002 PHE H 22 TRP 0.007 0.001 TRP G 199 HIS 0.003 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.35 (19386) covalent geometry : angle 0.77720 / 0.52 (26403) hydrogen bonds : bond 0.14466 / 15.23 ( 798) hydrogen bonds : angle 6.06588 / 6.76 ( 2280) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 301 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 245 MET cc_start: 0.4649 (mtt) cc_final: 0.3292 (ptt) REVERT: L 128 MET cc_start: 0.1819 (tpp) cc_final: 0.1111 (ptt) outliers start: 5 outliers final: 1 residues processed: 306 average time/residue: 0.1608 time to fit residues: 72.9496 Evaluate side-chains 114 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 295 ASN A 11 ASN A 154 GLN G 11 HIS E 27 HIS E 55 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.147181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.097411 restraints weight = 52334.617| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 4.21 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19386 Z= 0.147 Angle : 0.552 7.778 26403 Z= 0.303 Chirality : 0.044 0.283 3065 Planarity : 0.004 0.062 3163 Dihedral : 13.636 169.835 3210 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.86 % Allowed : 6.39 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.18), residues: 2254 helix: 2.23 (0.17), residues: 876 sheet: 1.27 (0.22), residues: 494 loop : -1.06 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 133 TYR 0.017 0.001 TYR G 215 PHE 0.020 0.001 PHE N 109 TRP 0.007 0.001 TRP G 199 HIS 0.004 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (19386) covalent geometry : angle 0.55179 / 0.30 (26403) hydrogen bonds : bond 0.06058 / 6.44 ( 798) hydrogen bonds : angle 4.21354 / 4.97 ( 2280) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 96 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8137 (tmtt) REVERT: C 124 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6999 (ttt) REVERT: D 80 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8066 (tm-30) REVERT: D 91 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8501 (mppt) REVERT: D 112 MET cc_start: 0.8380 (mtp) cc_final: 0.7896 (mtp) REVERT: D 260 MET cc_start: 0.8400 (mtm) cc_final: 0.8191 (mtm) REVERT: A 124 MET cc_start: 0.8459 (tmm) cc_final: 0.7522 (tmm) REVERT: G 182 ARG cc_start: 0.7792 (pmt-80) cc_final: 0.7109 (ptt90) REVERT: E 78 GLN cc_start: 0.9052 (mp10) cc_final: 0.8826 (pm20) REVERT: E 150 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8011 (pp20) REVERT: E 227 TYR cc_start: 0.8092 (p90) cc_final: 0.7647 (p90) REVERT: E 245 MET cc_start: 0.5082 (mtt) cc_final: 0.3555 (ptt) REVERT: E 281 LYS cc_start: 0.9027 (tptp) cc_final: 0.8785 (ptmt) outliers start: 35 outliers final: 22 residues processed: 142 average time/residue: 0.1256 time to fit residues: 27.9107 Evaluate side-chains 124 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain K residue 128 MET Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 113 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 128 optimal weight: 2.9990 chunk 200 optimal weight: 30.0000 chunk 53 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 ASN E 27 HIS L 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.140490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.088737 restraints weight = 63117.563| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 4.68 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19386 Z= 0.203 Angle : 0.582 7.865 26403 Z= 0.319 Chirality : 0.045 0.183 3065 Planarity : 0.005 0.060 3163 Dihedral : 13.671 167.447 3210 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.80 % Allowed : 8.20 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.17), residues: 2254 helix: 1.89 (0.17), residues: 886 sheet: 1.08 (0.23), residues: 470 loop : -1.25 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 28 TYR 0.015 0.002 TYR E 292 PHE 0.022 0.002 PHE C 159 TRP 0.009 0.001 TRP G 199 HIS 0.045 0.004 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (19386) covalent geometry : angle 0.58194 / 0.32 (26403) hydrogen bonds : bond 0.05428 / 5.77 ( 798) hydrogen bonds : angle 4.15205 / 4.95 ( 2280) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8421 (tmtt) REVERT: D 13 GLU cc_start: 0.6897 (tp30) cc_final: 0.6130 (tm-30) REVERT: D 80 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8109 (tm-30) REVERT: D 91 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8250 (mppt) REVERT: G 166 ARG cc_start: 0.9108 (mtp-110) cc_final: 0.8543 (mtp-110) REVERT: E 27 HIS cc_start: 0.7559 (OUTLIER) cc_final: 0.6915 (m-70) REVERT: E 78 GLN cc_start: 0.9069 (mp10) cc_final: 0.8812 (pm20) REVERT: E 150 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7985 (pp20) REVERT: E 227 TYR cc_start: 0.8393 (p90) cc_final: 0.7922 (p90) REVERT: E 245 MET cc_start: 0.5330 (mtt) cc_final: 0.3788 (ptt) REVERT: E 281 LYS cc_start: 0.9087 (tptp) cc_final: 0.8739 (tptt) REVERT: H 112 MET cc_start: 0.3568 (ptm) cc_final: 0.3001 (ptt) outliers start: 34 outliers final: 24 residues processed: 131 average time/residue: 0.1485 time to fit residues: 29.4366 Evaluate side-chains 125 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain K residue 128 MET Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 58 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 24 optimal weight: 0.7980 chunk 210 optimal weight: 5.9990 chunk 117 optimal weight: 0.0770 chunk 149 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 200 optimal weight: 30.0000 chunk 206 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 189 optimal weight: 8.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 295 ASN A 16 ASN E 27 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.142233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.090467 restraints weight = 43653.667| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 4.30 r_work: 0.3408 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19386 Z= 0.105 Angle : 0.473 8.132 26403 Z= 0.259 Chirality : 0.042 0.191 3065 Planarity : 0.004 0.051 3163 Dihedral : 13.452 166.485 3209 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 9.02 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2254 helix: 2.08 (0.17), residues: 887 sheet: 1.13 (0.23), residues: 474 loop : -1.20 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 28 TYR 0.014 0.001 TYR E 227 PHE 0.014 0.001 PHE C 159 TRP 0.007 0.001 TRP G 199 HIS 0.018 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (19386) covalent geometry : angle 0.47320 / 0.26 (26403) hydrogen bonds : bond 0.04256 / 4.53 ( 798) hydrogen bonds : angle 3.81153 / 4.49 ( 2280) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8358 (tmtt) REVERT: C 124 MET cc_start: 0.8223 (ttt) cc_final: 0.8021 (ttt) REVERT: D 80 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8271 (tm-30) REVERT: D 91 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8368 (mppt) REVERT: A 124 MET cc_start: 0.8775 (tmm) cc_final: 0.8511 (tmm) REVERT: G 182 ARG cc_start: 0.7709 (pmt-80) cc_final: 0.7382 (ppt90) REVERT: E 78 GLN cc_start: 0.9146 (mp10) cc_final: 0.8742 (pm20) REVERT: E 142 MET cc_start: 0.6956 (ttt) cc_final: 0.6737 (ttt) REVERT: E 150 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7966 (pp20) REVERT: E 184 TYR cc_start: 0.6393 (m-80) cc_final: 0.6130 (m-80) REVERT: E 227 TYR cc_start: 0.8384 (p90) cc_final: 0.7940 (p90) REVERT: E 245 MET cc_start: 0.5432 (mtt) cc_final: 0.3844 (ptt) REVERT: E 281 LYS cc_start: 0.9146 (tptp) cc_final: 0.8868 (ptmt) REVERT: L 112 MET cc_start: -0.1820 (ptt) cc_final: -0.2373 (ttp) outliers start: 25 outliers final: 17 residues processed: 118 average time/residue: 0.1225 time to fit residues: 22.8610 Evaluate side-chains 115 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain K residue 128 MET Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 58 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 106 optimal weight: 4.9990 chunk 216 optimal weight: 30.0000 chunk 161 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 152 optimal weight: 0.0670 chunk 206 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.141162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.088860 restraints weight = 63007.648| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 5.74 r_work: 0.3350 rms_B_bonded: 5.71 restraints_weight: 2.0000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19386 Z= 0.117 Angle : 0.479 11.421 26403 Z= 0.256 Chirality : 0.042 0.176 3065 Planarity : 0.004 0.048 3163 Dihedral : 13.308 165.591 3209 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.34 % Allowed : 9.33 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.18), residues: 2254 helix: 2.22 (0.17), residues: 887 sheet: 1.03 (0.23), residues: 490 loop : -1.13 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 166 TYR 0.017 0.001 TYR E 227 PHE 0.014 0.001 PHE C 159 TRP 0.008 0.001 TRP G 192 HIS 0.007 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (19386) covalent geometry : angle 0.47858 / 0.26 (26403) hydrogen bonds : bond 0.04050 / 4.30 ( 798) hydrogen bonds : angle 3.71042 / 4.38 ( 2280) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8477 (tmtt) REVERT: D 13 GLU cc_start: 0.7143 (tp30) cc_final: 0.6555 (tm-30) REVERT: D 80 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8332 (tm-30) REVERT: D 91 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8300 (mppt) REVERT: A 124 MET cc_start: 0.8762 (tmm) cc_final: 0.8466 (tmm) REVERT: G 182 ARG cc_start: 0.7741 (pmt-80) cc_final: 0.7397 (ppt90) REVERT: E 78 GLN cc_start: 0.9110 (mp10) cc_final: 0.8825 (pm20) REVERT: E 124 MET cc_start: 0.8067 (ptm) cc_final: 0.7596 (ptm) REVERT: E 142 MET cc_start: 0.6751 (ttt) cc_final: 0.6468 (ttt) REVERT: E 150 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7947 (pp20) REVERT: E 184 TYR cc_start: 0.6088 (m-80) cc_final: 0.5765 (m-80) REVERT: E 227 TYR cc_start: 0.8519 (p90) cc_final: 0.8091 (p90) REVERT: E 245 MET cc_start: 0.5765 (mtt) cc_final: 0.4637 (ptt) REVERT: E 281 LYS cc_start: 0.9011 (tptp) cc_final: 0.8725 (ptmt) outliers start: 25 outliers final: 18 residues processed: 124 average time/residue: 0.1409 time to fit residues: 27.5673 Evaluate side-chains 117 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 113 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 215 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 213 optimal weight: 0.0570 chunk 87 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 177 optimal weight: 30.0000 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 HIS L 140 GLN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.138322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.084667 restraints weight = 59316.450| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 5.33 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19386 Z= 0.196 Angle : 0.534 11.063 26403 Z= 0.286 Chirality : 0.043 0.208 3065 Planarity : 0.004 0.050 3163 Dihedral : 13.340 164.285 3209 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.55 % Allowed : 10.21 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2254 helix: 2.10 (0.17), residues: 886 sheet: 0.92 (0.23), residues: 478 loop : -1.23 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 166 TYR 0.018 0.001 TYR E 227 PHE 0.019 0.002 PHE C 159 TRP 0.010 0.002 TRP G 192 HIS 0.010 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (19386) covalent geometry : angle 0.53421 / 0.29 (26403) hydrogen bonds : bond 0.04574 / 4.82 ( 798) hydrogen bonds : angle 3.86113 / 4.61 ( 2280) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8572 (tmtt) REVERT: C 124 MET cc_start: 0.7759 (ttt) cc_final: 0.7334 (ttt) REVERT: D 13 GLU cc_start: 0.6937 (tp30) cc_final: 0.6708 (tm-30) REVERT: D 15 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6763 (mp) REVERT: D 91 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8203 (mppt) REVERT: A 1 MET cc_start: 0.8410 (ttp) cc_final: 0.7937 (ttp) REVERT: A 124 MET cc_start: 0.8359 (tmm) cc_final: 0.7987 (tmm) REVERT: G 182 ARG cc_start: 0.7736 (pmt-80) cc_final: 0.7409 (ppt90) REVERT: E 78 GLN cc_start: 0.9138 (mp10) cc_final: 0.8881 (pm20) REVERT: E 124 MET cc_start: 0.7847 (ptm) cc_final: 0.7565 (ptm) REVERT: E 142 MET cc_start: 0.7707 (ttt) cc_final: 0.7355 (ttt) REVERT: E 150 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8032 (pp20) REVERT: E 184 TYR cc_start: 0.6551 (m-80) cc_final: 0.6242 (m-80) REVERT: E 227 TYR cc_start: 0.8607 (p90) cc_final: 0.8201 (p90) REVERT: E 245 MET cc_start: 0.5976 (mtt) cc_final: 0.5116 (ptt) REVERT: E 281 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8691 (ptmt) outliers start: 29 outliers final: 20 residues processed: 119 average time/residue: 0.1286 time to fit residues: 24.5491 Evaluate side-chains 119 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain N residue 53 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 163 optimal weight: 6.9990 chunk 195 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 81 optimal weight: 0.0270 chunk 110 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.134989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.082092 restraints weight = 63960.860| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 5.24 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 19386 Z= 0.273 Angle : 0.652 13.973 26403 Z= 0.347 Chirality : 0.047 0.241 3065 Planarity : 0.005 0.061 3163 Dihedral : 13.506 161.917 3209 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.75 % Allowed : 10.93 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2254 helix: 1.68 (0.17), residues: 882 sheet: 0.37 (0.23), residues: 486 loop : -1.53 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 166 TYR 0.019 0.002 TYR L 119 PHE 0.027 0.002 PHE C 159 TRP 0.018 0.002 TRP G 192 HIS 0.018 0.003 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.27 (19386) covalent geometry : angle 0.65245 / 0.35 (26403) hydrogen bonds : bond 0.05521 / 5.81 ( 798) hydrogen bonds : angle 4.22635 / 5.11 ( 2280) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: C 96 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8678 (tptm) REVERT: C 178 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8301 (mt-10) REVERT: D 91 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8139 (mppt) REVERT: A 124 MET cc_start: 0.8446 (tmm) cc_final: 0.8063 (tmm) REVERT: A 187 SER cc_start: 0.8332 (p) cc_final: 0.7939 (m) REVERT: E 78 GLN cc_start: 0.9102 (mp10) cc_final: 0.8871 (pm20) REVERT: E 96 LYS cc_start: 0.9246 (mmtt) cc_final: 0.8955 (tptp) REVERT: E 124 MET cc_start: 0.7940 (ptm) cc_final: 0.7496 (ptm) REVERT: E 142 MET cc_start: 0.7598 (ttt) cc_final: 0.7315 (ttt) REVERT: E 150 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8085 (pp20) REVERT: E 204 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8530 (mmmt) REVERT: E 245 MET cc_start: 0.6398 (mtt) cc_final: 0.5658 (ptt) outliers start: 33 outliers final: 20 residues processed: 124 average time/residue: 0.1293 time to fit residues: 25.8681 Evaluate side-chains 114 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain N residue 53 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 20.0000 chunk 162 optimal weight: 0.0770 chunk 171 optimal weight: 6.9990 chunk 202 optimal weight: 20.0000 chunk 204 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 16 ASN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.136849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.085728 restraints weight = 62098.292| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 4.65 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19386 Z= 0.134 Angle : 0.507 9.047 26403 Z= 0.274 Chirality : 0.042 0.225 3065 Planarity : 0.004 0.046 3163 Dihedral : 13.341 163.609 3209 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.34 % Allowed : 11.49 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.18), residues: 2254 helix: 2.05 (0.17), residues: 880 sheet: 0.61 (0.24), residues: 476 loop : -1.35 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 166 TYR 0.026 0.001 TYR N 119 PHE 0.018 0.001 PHE C 159 TRP 0.012 0.001 TRP G 192 HIS 0.005 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (19386) covalent geometry : angle 0.50745 / 0.27 (26403) hydrogen bonds : bond 0.04203 / 4.43 ( 798) hydrogen bonds : angle 3.83650 / 4.58 ( 2280) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6725 (tp30) REVERT: D 91 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8226 (mppt) REVERT: A 1 MET cc_start: 0.8464 (ttp) cc_final: 0.7937 (ttp) REVERT: A 124 MET cc_start: 0.8363 (tmm) cc_final: 0.8004 (tmm) REVERT: A 187 SER cc_start: 0.8492 (p) cc_final: 0.8015 (m) REVERT: E 78 GLN cc_start: 0.9073 (mp10) cc_final: 0.8864 (pm20) REVERT: E 124 MET cc_start: 0.7916 (ptm) cc_final: 0.7512 (ptm) REVERT: E 150 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7978 (pp20) REVERT: E 245 MET cc_start: 0.6231 (mtt) cc_final: 0.4443 (ptt) REVERT: E 281 LYS cc_start: 0.9115 (tptp) cc_final: 0.8849 (ptmt) outliers start: 25 outliers final: 13 residues processed: 122 average time/residue: 0.1143 time to fit residues: 22.8441 Evaluate side-chains 106 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain N residue 53 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 86 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 85 optimal weight: 0.0000 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.138464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.088496 restraints weight = 43317.529| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.76 r_work: 0.3370 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19386 Z= 0.102 Angle : 0.494 10.835 26403 Z= 0.261 Chirality : 0.042 0.243 3065 Planarity : 0.003 0.044 3163 Dihedral : 13.192 164.586 3209 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.98 % Allowed : 11.96 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 2254 helix: 2.24 (0.17), residues: 882 sheet: 0.77 (0.24), residues: 476 loop : -1.21 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 166 TYR 0.021 0.001 TYR E 227 PHE 0.014 0.001 PHE C 159 TRP 0.009 0.001 TRP G 12 HIS 0.003 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (19386) covalent geometry : angle 0.49432 / 0.26 (26403) hydrogen bonds : bond 0.03700 / 3.89 ( 798) hydrogen bonds : angle 3.66203 / 4.35 ( 2280) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6771 (tp30) REVERT: C 124 MET cc_start: 0.8151 (ttt) cc_final: 0.7850 (ttm) REVERT: D 13 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7025 (pp20) REVERT: D 80 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8325 (tm-30) REVERT: D 91 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8231 (mppt) REVERT: A 1 MET cc_start: 0.8395 (ttp) cc_final: 0.7917 (ttp) REVERT: A 124 MET cc_start: 0.8717 (tmm) cc_final: 0.8414 (tmm) REVERT: A 187 SER cc_start: 0.8495 (p) cc_final: 0.7962 (m) REVERT: E 78 GLN cc_start: 0.9145 (mp10) cc_final: 0.8901 (pm20) REVERT: E 150 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7977 (pp20) REVERT: E 227 TYR cc_start: 0.8428 (p90) cc_final: 0.8112 (p90) REVERT: E 245 MET cc_start: 0.6293 (mtt) cc_final: 0.4304 (ptt) REVERT: E 281 LYS cc_start: 0.9105 (tptp) cc_final: 0.8817 (ptmt) outliers start: 18 outliers final: 12 residues processed: 115 average time/residue: 0.1312 time to fit residues: 24.3200 Evaluate side-chains 111 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 53 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 140 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 124 optimal weight: 0.3980 chunk 224 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 192 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 16 ASN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.138404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.088370 restraints weight = 51150.096| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 4.17 r_work: 0.3361 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19386 Z= 0.101 Angle : 0.489 10.698 26403 Z= 0.257 Chirality : 0.041 0.229 3065 Planarity : 0.003 0.042 3163 Dihedral : 13.134 165.443 3209 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.98 % Allowed : 11.96 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 2254 helix: 2.29 (0.17), residues: 882 sheet: 0.70 (0.24), residues: 484 loop : -1.14 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 166 TYR 0.021 0.001 TYR E 227 PHE 0.013 0.001 PHE G 185 TRP 0.008 0.001 TRP G 12 HIS 0.003 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (19386) covalent geometry : angle 0.48876 / 0.26 (26403) hydrogen bonds : bond 0.03580 / 3.76 ( 798) hydrogen bonds : angle 3.62313 / 4.33 ( 2280) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6804 (tp30) REVERT: D 13 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6838 (pp20) REVERT: D 80 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8332 (tm-30) REVERT: D 91 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8174 (mppt) REVERT: A 1 MET cc_start: 0.8402 (ttp) cc_final: 0.7910 (ttp) REVERT: A 124 MET cc_start: 0.8697 (tmm) cc_final: 0.8409 (tmm) REVERT: A 187 SER cc_start: 0.8525 (p) cc_final: 0.7939 (m) REVERT: E 78 GLN cc_start: 0.9148 (mp10) cc_final: 0.8904 (pm20) REVERT: E 124 MET cc_start: 0.8231 (ptm) cc_final: 0.7955 (ptm) REVERT: E 150 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7974 (pp20) REVERT: E 227 TYR cc_start: 0.8477 (p90) cc_final: 0.8137 (p90) REVERT: E 245 MET cc_start: 0.6702 (mtt) cc_final: 0.4351 (ptt) REVERT: E 281 LYS cc_start: 0.9100 (tptp) cc_final: 0.8824 (ptmt) outliers start: 18 outliers final: 12 residues processed: 113 average time/residue: 0.1353 time to fit residues: 24.6615 Evaluate side-chains 109 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 53 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 14 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 142 optimal weight: 0.0170 chunk 218 optimal weight: 0.0870 chunk 167 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 16 ASN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.139004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.089243 restraints weight = 48402.652| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.73 r_work: 0.3386 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19386 Z= 0.094 Angle : 0.475 10.387 26403 Z= 0.248 Chirality : 0.041 0.225 3065 Planarity : 0.003 0.038 3163 Dihedral : 13.088 166.576 3209 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.98 % Allowed : 12.01 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 2254 helix: 2.37 (0.17), residues: 884 sheet: 0.79 (0.24), residues: 484 loop : -1.06 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 166 TYR 0.022 0.001 TYR E 227 PHE 0.010 0.001 PHE C 159 TRP 0.009 0.001 TRP G 12 HIS 0.003 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (19386) covalent geometry : angle 0.47463 / 0.25 (26403) hydrogen bonds : bond 0.03391 / 3.55 ( 798) hydrogen bonds : angle 3.52295 / 4.19 ( 2280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8088.12 seconds wall clock time: 137 minutes 50.13 seconds (8270.13 seconds total)