Starting phenix.real_space_refine on Thu Feb 5 19:08:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9crq_45875/02_2026/9crq_45875.cif Found real_map, /net/cci-nas-00/data/ceres_data/9crq_45875/02_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_45875/02_2026/9crq_45875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9crq_45875/02_2026/9crq_45875.map" model { file = "/net/cci-nas-00/data/ceres_data/9crq_45875/02_2026/9crq_45875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9crq_45875/02_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-2.0-5952/lib/python3.9/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: 4.22, per 1000 atoms: 0.22 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: 1.17 Conformation dependent library (CDL) restraints added in 686.9 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: 1.92 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: 2.24 Time building geometry restraints manager: 1.50 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=" 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=" CZ ARG L 111 " pdb=" NH2 ARG L 111 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.39e+00 bond pdb=" CZ ARG H 52 " pdb=" NH2 ARG H 52 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.36e+00 ... (remaining 19381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 24294 1.35 - 2.69: 1669 2.69 - 4.04: 395 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=" OE1 GLN N 55 " pdb=" CD GLN N 55 " pdb=" NE2 GLN N 55 " ideal model delta sigma weight residual 122.60 118.90 3.70 1.00e+00 1.00e+00 1.37e+01 angle pdb=" C ALA N 123 " pdb=" N GLY N 124 " pdb=" CA GLY N 124 " ideal model delta sigma weight residual 119.98 124.07 -4.09 1.11e+00 8.12e-01 1.36e+01 angle pdb=" C VAL H 117 " pdb=" N TYR H 118 " pdb=" CA TYR H 118 " ideal model delta sigma weight residual 120.38 125.34 -4.96 1.37e+00 5.33e-01 1.31e+01 angle pdb=" CA VAL N 117 " pdb=" CB VAL N 117 " pdb=" CG1 VAL N 117 " ideal model delta sigma weight residual 110.40 116.54 -6.14 1.70e+00 3.46e-01 1.30e+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: 2645 0.075 - 0.149: 399 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 16.570 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 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= 0.330 Angle : 0.761 6.731 26403 Z= 0.488 Chirality : 0.050 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 covalent geometry : bond 0.00583 (19386) covalent geometry : angle 0.76122 (26403) hydrogen bonds : bond 0.14466 ( 798) hydrogen bonds : angle 6.06588 ( 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 : 0.512 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: 0.3293 (ptt) REVERT: L 128 MET cc_start: 0.1819 (tpp) cc_final: 0.1110 (ptt) outliers start: 5 outliers final: 1 residues processed: 306 average time/residue: 0.1431 time to fit residues: 65.2196 Evaluate side-chains 113 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 295 ASN A 11 ASN A 16 ASN A 154 GLN G 11 HIS E 27 HIS E 55 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.145177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.095283 restraints weight = 52073.666| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 4.12 r_work: 0.3480 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19386 Z= 0.128 Angle : 0.529 8.493 26403 Z= 0.279 Chirality : 0.042 0.164 3065 Planarity : 0.004 0.062 3163 Dihedral : 13.543 165.617 3210 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.70 % Allowed : 6.39 % Favored : 91.91 % 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: 1.29 (0.18), residues: 2254 helix: 2.37 (0.17), residues: 872 sheet: 1.39 (0.23), residues: 482 loop : -1.04 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 13 TYR 0.019 0.001 TYR G 215 PHE 0.015 0.001 PHE A 163 TRP 0.010 0.002 TRP G 138 HIS 0.004 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00284 (19386) covalent geometry : angle 0.52924 (26403) hydrogen bonds : bond 0.04619 ( 798) hydrogen bonds : angle 3.91624 ( 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 149 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 96 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8221 (tmtt) REVERT: D 80 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8310 (tm-30) REVERT: D 91 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8306 (mppt) REVERT: D 119 ASP cc_start: 0.8645 (t0) cc_final: 0.8072 (m-30) REVERT: A 1 MET cc_start: 0.8153 (ttp) cc_final: 0.7830 (ttp) REVERT: A 112 MET cc_start: 0.8031 (mtp) cc_final: 0.7644 (ttt) REVERT: A 124 MET cc_start: 0.8719 (tmm) cc_final: 0.8369 (tmm) REVERT: G 182 ARG cc_start: 0.7958 (pmt-80) cc_final: 0.7598 (ppt90) REVERT: E 78 GLN cc_start: 0.9105 (mp10) cc_final: 0.8902 (pm20) REVERT: E 150 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7988 (pp20) REVERT: E 227 TYR cc_start: 0.8362 (p90) cc_final: 0.8011 (p90) REVERT: E 245 MET cc_start: 0.5399 (mtt) cc_final: 0.3604 (ptt) outliers start: 32 outliers final: 16 residues processed: 140 average time/residue: 0.1478 time to fit residues: 32.2236 Evaluate side-chains 115 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 295 ASN Chi-restraints excluded: chain C residue 251 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 D residue 311 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain N residue 58 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: 6.9990 chunk 53 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 109 optimal weight: 0.0030 chunk 134 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 295 ASN D 16 ASN A 16 ASN L 140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.140748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.087954 restraints weight = 62729.958| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 5.29 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19386 Z= 0.143 Angle : 0.514 7.820 26403 Z= 0.273 Chirality : 0.042 0.220 3065 Planarity : 0.004 0.057 3163 Dihedral : 13.369 163.086 3210 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.86 % Allowed : 7.94 % Favored : 90.21 % 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: 1.14 (0.18), residues: 2254 helix: 2.17 (0.17), residues: 891 sheet: 1.24 (0.23), residues: 473 loop : -1.05 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 166 TYR 0.013 0.001 TYR G 215 PHE 0.018 0.001 PHE C 159 TRP 0.013 0.002 TRP G 192 HIS 0.041 0.003 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00328 (19386) covalent geometry : angle 0.51441 (26403) hydrogen bonds : bond 0.04261 ( 798) hydrogen bonds : angle 3.80167 ( 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 136 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 295 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7251 (t0) REVERT: C 21 ILE cc_start: 0.8690 (mt) cc_final: 0.8474 (mm) REVERT: C 26 LYS cc_start: 0.8816 (mtpp) cc_final: 0.8592 (mtpp) REVERT: C 96 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8473 (tmtt) REVERT: D 80 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8116 (tm-30) REVERT: D 91 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8275 (mppt) REVERT: A 1 MET cc_start: 0.8245 (ttp) cc_final: 0.8039 (ttp) REVERT: A 124 MET cc_start: 0.8305 (tmm) cc_final: 0.7865 (tmm) REVERT: G 182 ARG cc_start: 0.7573 (pmt-80) cc_final: 0.7313 (ppt90) REVERT: E 78 GLN cc_start: 0.9127 (mp10) cc_final: 0.8913 (pm20) REVERT: E 150 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8008 (pp20) REVERT: E 227 TYR cc_start: 0.8612 (p90) cc_final: 0.8286 (p90) REVERT: E 245 MET cc_start: 0.5721 (mtt) cc_final: 0.5007 (ptt) REVERT: H 112 MET cc_start: 0.4025 (ptp) cc_final: 0.3186 (ptt) outliers start: 35 outliers final: 22 residues processed: 127 average time/residue: 0.1511 time to fit residues: 29.1832 Evaluate side-chains 117 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 295 ASN 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 91 LYS 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 201 PHE Chi-restraints excluded: chain G residue 180 VAL 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 L residue 117 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 112 MET Chi-restraints excluded: chain N residue 113 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 24 optimal weight: 0.5980 chunk 210 optimal weight: 30.0000 chunk 117 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 206 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 189 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN E 27 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.138665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.088386 restraints weight = 44046.160| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.55 r_work: 0.3368 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 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 = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19386 Z= 0.148 Angle : 0.501 7.169 26403 Z= 0.265 Chirality : 0.042 0.215 3065 Planarity : 0.004 0.048 3163 Dihedral : 13.402 161.338 3210 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.80 % Allowed : 9.07 % Favored : 89.12 % 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: 1.08 (0.18), residues: 2254 helix: 2.25 (0.17), residues: 886 sheet: 0.99 (0.23), residues: 482 loop : -1.09 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 43 TYR 0.016 0.001 TYR E 227 PHE 0.018 0.001 PHE C 159 TRP 0.012 0.001 TRP G 192 HIS 0.021 0.002 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00342 (19386) covalent geometry : angle 0.50134 (26403) hydrogen bonds : bond 0.03982 ( 798) hydrogen bonds : angle 3.68938 ( 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 135 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 295 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7513 (t0) REVERT: C 13 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7323 (pp20) REVERT: C 96 LYS cc_start: 0.8973 (mmtt) cc_final: 0.8749 (tmtt) REVERT: D 91 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8336 (mppt) REVERT: A 1 MET cc_start: 0.8404 (ttp) cc_final: 0.8055 (mtp) REVERT: A 124 MET cc_start: 0.8657 (tmm) cc_final: 0.8398 (tmm) REVERT: G 166 ARG cc_start: 0.8803 (mtp-110) cc_final: 0.8595 (mtp-110) REVERT: G 182 ARG cc_start: 0.7658 (pmt-80) cc_final: 0.7328 (ppt90) REVERT: E 27 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.7193 (m-70) REVERT: E 78 GLN cc_start: 0.9202 (mp10) cc_final: 0.8990 (pm20) REVERT: E 150 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7976 (pp20) REVERT: E 245 MET cc_start: 0.5588 (mtt) cc_final: 0.3667 (ptt) REVERT: E 313 ASP cc_start: 0.9401 (m-30) cc_final: 0.8823 (p0) REVERT: E 314 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8517 (pp) outliers start: 34 outliers final: 18 residues processed: 126 average time/residue: 0.1431 time to fit residues: 28.8293 Evaluate side-chains 114 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 177 VAL 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 161 VAL Chi-restraints excluded: chain D residue 180 SER 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 G residue 180 VAL 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 N residue 113 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 106 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 201 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 HIS B 295 ASN E 27 HIS L 140 GLN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.133576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.082355 restraints weight = 64033.473| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 4.62 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 19386 Z= 0.312 Angle : 0.672 8.146 26403 Z= 0.354 Chirality : 0.046 0.234 3065 Planarity : 0.005 0.057 3163 Dihedral : 13.739 160.799 3209 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.75 % Allowed : 10.36 % Favored : 87.89 % 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: 0.32 (0.17), residues: 2254 helix: 1.69 (0.17), residues: 884 sheet: 0.39 (0.23), residues: 468 loop : -1.43 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 136 TYR 0.017 0.002 TYR C 125 PHE 0.026 0.002 PHE C 159 TRP 0.023 0.003 TRP G 192 HIS 0.024 0.003 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00729 (19386) covalent geometry : angle 0.67222 (26403) hydrogen bonds : bond 0.05533 ( 798) hydrogen bonds : angle 4.24907 ( 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 130 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: C 13 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7569 (pp20) REVERT: D 91 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8259 (mppt) REVERT: A 1 MET cc_start: 0.8171 (ttp) cc_final: 0.7725 (ttp) REVERT: G 166 ARG cc_start: 0.8869 (mtp-110) cc_final: 0.8548 (mtp-110) REVERT: E 1 MET cc_start: 0.7704 (mtp) cc_final: 0.7428 (mtp) REVERT: E 27 HIS cc_start: 0.8337 (OUTLIER) cc_final: 0.7570 (m-70) REVERT: E 112 MET cc_start: 0.9327 (mtm) cc_final: 0.9119 (ptm) REVERT: E 124 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7446 (ptm) REVERT: E 150 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7944 (pp20) REVERT: E 245 MET cc_start: 0.5725 (mtt) cc_final: 0.4354 (ptt) outliers start: 33 outliers final: 20 residues processed: 121 average time/residue: 0.1397 time to fit residues: 27.0414 Evaluate side-chains 115 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 177 VAL 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 311 VAL 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 E residue 27 HIS Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain N residue 53 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: 8.9990 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 177 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 27 HIS ** 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 = 0.4344 r_free = 0.4344 target = 0.134075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.082324 restraints weight = 60254.675| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 5.00 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 19386 Z= 0.237 Angle : 0.585 7.914 26403 Z= 0.309 Chirality : 0.044 0.212 3065 Planarity : 0.004 0.057 3163 Dihedral : 13.664 165.093 3209 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.96 % Allowed : 11.24 % Favored : 86.80 % 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: 0.28 (0.17), residues: 2254 helix: 1.77 (0.17), residues: 882 sheet: 0.27 (0.23), residues: 472 loop : -1.51 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 136 TYR 0.015 0.001 TYR E 227 PHE 0.021 0.002 PHE C 159 TRP 0.016 0.002 TRP G 192 HIS 0.021 0.002 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00558 (19386) covalent geometry : angle 0.58539 (26403) hydrogen bonds : bond 0.04649 ( 798) hydrogen bonds : angle 4.06559 ( 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 130 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7643 (pp20) REVERT: C 90 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7577 (mp) REVERT: D 91 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8183 (mppt) REVERT: A 1 MET cc_start: 0.8195 (ttp) cc_final: 0.7746 (ttp) REVERT: A 149 ASP cc_start: 0.7979 (t0) cc_final: 0.7644 (t0) REVERT: E 1 MET cc_start: 0.7725 (mtp) cc_final: 0.7501 (mtp) REVERT: E 27 HIS cc_start: 0.8102 (t-90) cc_final: 0.7427 (m-70) REVERT: E 150 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7952 (pp20) REVERT: E 245 MET cc_start: 0.5742 (mtt) cc_final: 0.4784 (ptp) outliers start: 37 outliers final: 28 residues processed: 124 average time/residue: 0.1267 time to fit residues: 25.6416 Evaluate side-chains 118 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 287 ASN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 64 ILE 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 180 SER 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 18 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 180 SER Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 113 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 163 optimal weight: 7.9990 chunk 195 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 HIS H 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.133692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.083042 restraints weight = 63750.705| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.58 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19386 Z= 0.206 Angle : 0.558 7.556 26403 Z= 0.294 Chirality : 0.043 0.198 3065 Planarity : 0.004 0.047 3163 Dihedral : 13.579 169.569 3209 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.32 % Allowed : 11.03 % Favored : 86.65 % 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: 0.31 (0.18), residues: 2254 helix: 1.78 (0.17), residues: 886 sheet: 0.26 (0.23), residues: 472 loop : -1.47 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 166 TYR 0.015 0.001 TYR E 227 PHE 0.019 0.002 PHE G 185 TRP 0.014 0.002 TRP G 192 HIS 0.009 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00484 (19386) covalent geometry : angle 0.55806 (26403) hydrogen bonds : bond 0.04431 ( 798) hydrogen bonds : angle 3.97219 ( 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 134 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 90 time to evaluate : 0.620 Fit side-chains REVERT: B 262 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: C 13 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7634 (pp20) REVERT: D 91 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8163 (mppt) REVERT: A 1 MET cc_start: 0.8197 (ttp) cc_final: 0.7708 (ttp) REVERT: A 149 ASP cc_start: 0.7854 (t0) cc_final: 0.7550 (t0) REVERT: E 1 MET cc_start: 0.7922 (mtp) cc_final: 0.7456 (mtp) REVERT: E 124 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7336 (ptm) REVERT: E 150 GLU cc_start: 0.8214 (mt-10) cc_final: 0.8001 (pp20) REVERT: E 227 TYR cc_start: 0.8715 (p90) cc_final: 0.8331 (p90) REVERT: E 245 MET cc_start: 0.6393 (mtt) cc_final: 0.5619 (mtm) outliers start: 44 outliers final: 33 residues processed: 128 average time/residue: 0.1139 time to fit residues: 24.0916 Evaluate side-chains 124 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 250 LEU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 13 GLU 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 301 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 64 ILE 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 180 SER 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 18 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 113 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: 4.9990 chunk 171 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 175 optimal weight: 0.0970 chunk 143 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.134658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.084237 restraints weight = 62608.693| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.99 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5260 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= 0.150 Angle : 0.512 10.532 26403 Z= 0.268 Chirality : 0.041 0.176 3065 Planarity : 0.004 0.044 3163 Dihedral : 13.465 170.379 3209 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.86 % Allowed : 11.86 % Favored : 86.29 % 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: 0.50 (0.18), residues: 2254 helix: 2.01 (0.17), residues: 884 sheet: 0.25 (0.24), residues: 478 loop : -1.38 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 166 TYR 0.014 0.001 TYR E 227 PHE 0.017 0.001 PHE G 185 TRP 0.010 0.001 TRP G 192 HIS 0.007 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00349 (19386) covalent geometry : angle 0.51184 (26403) hydrogen bonds : bond 0.03874 ( 798) hydrogen bonds : angle 3.80896 ( 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 120 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.620 Fit side-chains REVERT: B 96 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8446 (tptp) REVERT: B 262 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8070 (pm20) REVERT: D 91 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8108 (mppt) REVERT: A 1 MET cc_start: 0.8332 (ttp) cc_final: 0.7819 (ttp) REVERT: A 149 ASP cc_start: 0.7745 (t0) cc_final: 0.7413 (t0) REVERT: E 1 MET cc_start: 0.7639 (mtp) cc_final: 0.7274 (mtp) REVERT: E 124 MET cc_start: 0.7639 (ttp) cc_final: 0.7139 (ptm) REVERT: E 150 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8022 (pp20) REVERT: E 227 TYR cc_start: 0.8864 (p90) cc_final: 0.8497 (p90) outliers start: 35 outliers final: 27 residues processed: 116 average time/residue: 0.1110 time to fit residues: 21.2710 Evaluate side-chains 114 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 45 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 180 SER 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 18 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 113 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 86 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 85 optimal weight: 0.0060 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.136056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.086734 restraints weight = 43557.562| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.45 r_work: 0.3333 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19386 Z= 0.109 Angle : 0.475 8.638 26403 Z= 0.248 Chirality : 0.040 0.147 3065 Planarity : 0.003 0.041 3163 Dihedral : 13.277 170.380 3209 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.60 % Allowed : 12.11 % Favored : 86.29 % 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: 0.80 (0.18), residues: 2254 helix: 2.27 (0.18), residues: 884 sheet: 0.47 (0.24), residues: 458 loop : -1.24 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 166 TYR 0.015 0.001 TYR E 227 PHE 0.014 0.001 PHE G 185 TRP 0.009 0.001 TRP G 12 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00250 (19386) covalent geometry : angle 0.47547 (26403) hydrogen bonds : bond 0.03370 ( 798) hydrogen bonds : angle 3.59964 ( 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 119 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.731 Fit side-chains REVERT: B 96 LYS cc_start: 0.8678 (mmmm) cc_final: 0.8416 (tptp) REVERT: B 262 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7921 (pm20) REVERT: C 124 MET cc_start: 0.8180 (ttt) cc_final: 0.7949 (ttt) REVERT: D 80 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8291 (tm-30) REVERT: D 91 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8238 (mppt) REVERT: A 1 MET cc_start: 0.8314 (ttp) cc_final: 0.7819 (ttp) REVERT: A 124 MET cc_start: 0.8799 (tmm) cc_final: 0.8538 (tmm) REVERT: E 1 MET cc_start: 0.7728 (mtp) cc_final: 0.7384 (mtp) REVERT: E 124 MET cc_start: 0.7839 (ttp) cc_final: 0.7511 (ptm) REVERT: E 227 TYR cc_start: 0.8713 (p90) cc_final: 0.8372 (p90) REVERT: E 245 MET cc_start: 0.4190 (mtm) cc_final: 0.2937 (ptt) REVERT: K 56 MET cc_start: 0.2810 (tmm) cc_final: 0.2391 (mtm) REVERT: H 105 ASP cc_start: 0.5447 (m-30) cc_final: 0.5007 (t70) outliers start: 30 outliers final: 24 residues processed: 115 average time/residue: 0.1309 time to fit residues: 24.8100 Evaluate side-chains 112 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 180 SER 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 G residue 217 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 113 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 140 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 228 optimal weight: 50.0000 chunk 65 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 224 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 192 optimal weight: 0.0010 chunk 57 optimal weight: 3.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.136245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.086420 restraints weight = 51375.264| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 4.53 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5314 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= 0.103 Angle : 0.478 11.797 26403 Z= 0.248 Chirality : 0.040 0.141 3065 Planarity : 0.003 0.038 3163 Dihedral : 13.192 170.218 3209 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.39 % Allowed : 12.32 % Favored : 86.29 % 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: 0.91 (0.18), residues: 2254 helix: 2.32 (0.18), residues: 885 sheet: 0.59 (0.24), residues: 452 loop : -1.17 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 166 TYR 0.014 0.001 TYR E 227 PHE 0.015 0.001 PHE G 185 TRP 0.009 0.001 TRP G 12 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00237 (19386) covalent geometry : angle 0.47828 (26403) hydrogen bonds : bond 0.03341 ( 798) hydrogen bonds : angle 3.55910 ( 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 116 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.567 Fit side-chains REVERT: B 96 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8336 (tptp) REVERT: B 262 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8051 (pm20) REVERT: C 124 MET cc_start: 0.7560 (ttt) cc_final: 0.7359 (ttt) REVERT: D 80 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8075 (tm-30) REVERT: D 91 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8111 (mppt) REVERT: A 1 MET cc_start: 0.8281 (ttp) cc_final: 0.7744 (ttp) REVERT: A 101 TYR cc_start: 0.7621 (m-80) cc_final: 0.7402 (m-80) REVERT: A 124 MET cc_start: 0.8496 (tmm) cc_final: 0.8208 (tmm) REVERT: A 149 ASP cc_start: 0.7754 (t0) cc_final: 0.7551 (t0) REVERT: E 1 MET cc_start: 0.7545 (mtp) cc_final: 0.7262 (mtp) REVERT: E 112 MET cc_start: 0.9346 (mtm) cc_final: 0.9139 (ptm) REVERT: E 227 TYR cc_start: 0.8940 (p90) cc_final: 0.8552 (p90) REVERT: E 245 MET cc_start: 0.4659 (mtm) cc_final: 0.4265 (ptt) REVERT: K 56 MET cc_start: 0.3014 (tmm) cc_final: 0.2614 (mtm) REVERT: H 105 ASP cc_start: 0.5334 (m-30) cc_final: 0.4912 (t70) outliers start: 26 outliers final: 23 residues processed: 113 average time/residue: 0.1310 time to fit residues: 24.0274 Evaluate side-chains 111 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 180 SER 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 219 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 113 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 14 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 113 optimal weight: 0.0060 chunk 94 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 0.0970 chunk 40 optimal weight: 0.6980 chunk 142 optimal weight: 0.1980 chunk 218 optimal weight: 0.0770 chunk 167 optimal weight: 0.0030 chunk 173 optimal weight: 3.9990 overall best weight: 0.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.140244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.090967 restraints weight = 48874.364| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.88 r_work: 0.3435 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19386 Z= 0.083 Angle : 0.453 9.821 26403 Z= 0.234 Chirality : 0.040 0.162 3065 Planarity : 0.003 0.033 3163 Dihedral : 12.968 168.985 3209 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.98 % Allowed : 12.63 % Favored : 86.39 % 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: 1.23 (0.18), residues: 2254 helix: 2.44 (0.18), residues: 894 sheet: 0.82 (0.25), residues: 450 loop : -0.88 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 166 TYR 0.016 0.001 TYR E 227 PHE 0.011 0.001 PHE G 185 TRP 0.014 0.002 TRP G 12 HIS 0.002 0.000 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00183 (19386) covalent geometry : angle 0.45251 (26403) hydrogen bonds : bond 0.02765 ( 798) hydrogen bonds : angle 3.35269 ( 2280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8775.73 seconds wall clock time: 149 minutes 35.37 seconds (8975.37 seconds total)