Starting phenix.real_space_refine on Sat Jul 4 09:07:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9crq_45875/07_2026/9crq_45875.cif Found real_map, /net/cci-nas-00/data/ceres_data/9crq_45875/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9crq_45875/07_2026/9crq_45875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9crq_45875/07_2026/9crq_45875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9crq_45875/07_2026/9crq_45875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9crq_45875/07_2026/9crq_45875.map" } 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18974 Number of models: 1 Model: "" Number of chains: 17 Chain: "M" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 373 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "S" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 740 Classifications: {'RNA': 35} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 11, 'rna3p_pur': 11, 'rna3p_pyr': 6} Link IDs: {'rna2p': 18, 'rna3p': 16} Chain: "B" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "C" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "A" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2448 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "G" Number of atoms: 1692 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1687 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 211, 1687 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 bond proxies already assigned to first conformer: 1722 Chain: "E" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2337 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain breaks: 1 Chain: "K" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Chain: "L" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain breaks: 1 Chain: "H" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1013 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Chain: "N" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Chain: "S" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.25 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: 1.79 Conformation dependent library (CDL) restraints added in 847.0 milliseconds 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4242 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 25 sheets defined 41.7% alpha, 16.6% beta 15 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'B' and resid 49 through 69 removed outlier: 4.292A pdb=" N LEU B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.926A pdb=" N GLN B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.555A pdb=" N LEU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.549A pdb=" N ASP B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 195 removed outlier: 3.635A pdb=" N ILE B 195 " --> pdb=" O GLU B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 195' Processing helix chain 'B' and resid 207 through 225 removed outlier: 3.638A pdb=" N LEU B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 4.310A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.548A pdb=" N ASN B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 320 removed outlier: 4.064A pdb=" N LEU B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 69 removed outlier: 4.289A pdb=" N LEU C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.927A pdb=" N GLN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.552A pdb=" N LEU C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 113 Processing helix chain 'C' and resid 115 through 122 removed outlier: 3.551A pdb=" N ASP C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 195 removed outlier: 3.635A pdb=" N ILE C 195 " --> pdb=" O GLU C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 192 through 195' Processing helix chain 'C' and resid 207 through 225 removed outlier: 3.637A pdb=" N LEU C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ALA C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 4.310A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.547A pdb=" N ASN C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 320 removed outlier: 4.062A pdb=" N LEU C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 69 removed outlier: 4.291A pdb=" N LEU D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 78 removed outlier: 3.926A pdb=" N GLN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.552A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.550A pdb=" N ASP D 119 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 195 removed outlier: 3.634A pdb=" N ILE D 195 " --> pdb=" O GLU D 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 192 through 195' Processing helix chain 'D' and resid 207 through 225 removed outlier: 3.637A pdb=" N LEU D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ALA D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 removed outlier: 4.311A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 285 removed outlier: 3.548A pdb=" N ASN D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 removed outlier: 4.064A pdb=" N LEU D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 69 removed outlier: 4.398A pdb=" N LEU A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.742A pdb=" N GLN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.567A pdb=" N ILE A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.678A pdb=" N ASP A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 225 removed outlier: 3.822A pdb=" N LEU A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYS A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 4.077A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.771A pdb=" N THR A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 320 removed outlier: 4.056A pdb=" N LEU A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 42 Processing helix chain 'G' and resid 129 through 138 Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.743A pdb=" N ILE G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 69 removed outlier: 4.161A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 removed outlier: 3.820A pdb=" N GLN E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 103 through 115 Processing helix chain 'E' and resid 115 through 121 removed outlier: 3.501A pdb=" N ASP E 119 " --> pdb=" O ASP E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 232 removed outlier: 3.559A pdb=" N LEU E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYS E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER E 228 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 284 removed outlier: 3.525A pdb=" N THR E 273 " --> pdb=" O TYR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 320 removed outlier: 3.769A pdb=" N LEU E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 26 Processing helix chain 'K' and resid 28 through 36 Processing helix chain 'K' and resid 39 through 60 Processing helix chain 'K' and resid 102 through 116 Processing helix chain 'K' and resid 117 through 144 removed outlier: 3.719A pdb=" N ARG K 121 " --> pdb=" O VAL K 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 26 Processing helix chain 'L' and resid 28 through 36 Processing helix chain 'L' and resid 39 through 60 Processing helix chain 'L' and resid 102 through 116 Processing helix chain 'L' and resid 117 through 145 removed outlier: 3.717A pdb=" N ARG L 121 " --> pdb=" O VAL L 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 26 Processing helix chain 'H' and resid 28 through 36 Processing helix chain 'H' and resid 39 through 60 Processing helix chain 'H' and resid 102 through 116 Processing helix chain 'H' and resid 117 through 144 removed outlier: 3.723A pdb=" N ARG H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 26 Processing helix chain 'N' and resid 28 through 37 Processing helix chain 'N' and resid 39 through 60 Processing helix chain 'N' and resid 102 through 116 Processing helix chain 'N' and resid 117 through 137 removed outlier: 3.661A pdb=" N ARG N 121 " --> pdb=" O VAL N 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2 through 13 current: chain 'B' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 174 through 190 current: chain 'B' and resid 289 through 295 removed outlier: 4.363A pdb=" N THR B 306 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 125 Processing sheet with id=AA4, first strand: chain 'C' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 2 through 13 current: chain 'C' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 174 through 190 current: chain 'C' and resid 289 through 295 removed outlier: 4.362A pdb=" N THR C 306 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 36 Processing sheet with id=AA6, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AA7, first strand: chain 'D' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 2 through 13 current: chain 'D' and resid 174 through 190 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 174 through 190 current: chain 'D' and resid 289 through 295 removed outlier: 4.360A pdb=" N THR D 306 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 29 through 36 Processing sheet with id=AA9, first strand: chain 'D' and resid 123 through 125 Processing sheet with id=AB1, first strand: chain 'A' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2 through 13 current: chain 'A' and resid 174 through 182 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 174 through 182 current: chain 'A' and resid 289 through 295 removed outlier: 3.699A pdb=" N THR A 306 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AB3, first strand: chain 'A' and resid 124 through 125 removed outlier: 3.573A pdb=" N VAL A 131 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 68 through 73 removed outlier: 3.838A pdb=" N ASN G 154 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS G 9 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL G 152 " --> pdb=" O LYS G 9 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 13 through 14 removed outlier: 3.643A pdb=" N PHE G 14 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 161 through 163 removed outlier: 3.736A pdb=" N LYS G 161 " --> pdb=" O GLU G 231 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER G 240 " --> pdb=" O GLU G 228 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR G 230 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL G 238 " --> pdb=" O TYR G 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AB8, first strand: chain 'G' and resid 173 through 174 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 173 through 174 current: chain 'G' and resid 205 through 213 removed outlier: 3.506A pdb=" N THR G 213 " --> pdb=" O ALA G 218 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA G 218 " --> pdb=" O THR G 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 2 through 13 current: chain 'E' and resid 178 through 190 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 178 through 190 current: chain 'E' and resid 289 through 295 removed outlier: 4.195A pdb=" N THR E 306 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 17 through 21 removed outlier: 4.293A pdb=" N LYS E 26 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N SER E 20 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU E 24 " --> pdb=" O SER E 20 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 29 through 36 Processing sheet with id=AC3, first strand: chain 'E' and resid 123 through 125 Processing sheet with id=AC4, first strand: chain 'K' and resid 63 through 69 Processing sheet with id=AC5, first strand: chain 'L' and resid 63 through 69 Processing sheet with id=AC6, first strand: chain 'H' and resid 63 through 69 Processing sheet with id=AC7, first strand: chain 'N' and resid 63 through 68 759 hydrogen bonds defined for protein. 2202 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5242 1.33 - 1.46: 4266 1.46 - 1.58: 9664 1.58 - 1.71: 103 1.71 - 1.83: 111 Bond restraints: 19386 Sorted by residual: bond pdb=" C3' DG M 7 " pdb=" C2' DG M 7 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.38e+01 bond pdb=" CZ ARG K 121 " pdb=" NH2 ARG K 121 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.52e+00 bond pdb=" CZ ARG N 52 " pdb=" NH2 ARG N 52 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.64e+00 bond pdb=" CZ ARG L 133 " pdb=" NH2 ARG L 133 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.59e+00 bond pdb=" C3' DC M 10 " pdb=" C2' DC M 10 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.41e+00 ... (remaining 19381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 24246 1.35 - 2.69: 1720 2.69 - 4.04: 392 4.04 - 5.38: 41 5.38 - 6.73: 4 Bond angle restraints: 26403 Sorted by residual: angle pdb=" C ASN E 11 " pdb=" N LEU E 12 " pdb=" CA LEU E 12 " ideal model delta sigma weight residual 122.93 129.66 -6.73 1.51e+00 4.39e-01 1.99e+01 angle pdb=" N3 DT M 17 " pdb=" C4 DT M 17 " pdb=" O4 DT M 17 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT M 15 " pdb=" C4 DT M 15 " pdb=" O4 DT M 15 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT M 16 " pdb=" C4 DT M 16 " pdb=" O4 DT M 16 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT M 14 " pdb=" C4 DT M 14 " pdb=" O4 DT M 14 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 26398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 11437 33.64 - 67.28: 291 67.28 - 100.92: 28 100.92 - 134.55: 0 134.55 - 168.19: 2 Dihedral angle restraints: 11758 sinusoidal: 5141 harmonic: 6617 Sorted by residual: dihedral pdb=" O4' U S 32 " pdb=" C1' U S 32 " pdb=" N1 U S 32 " pdb=" C2 U S 32 " ideal model delta sinusoidal sigma weight residual 232.00 135.36 96.64 1 1.70e+01 3.46e-03 3.71e+01 dihedral pdb=" O4' U S 2 " pdb=" C1' U S 2 " pdb=" N1 U S 2 " pdb=" C2 U S 2 " ideal model delta sinusoidal sigma weight residual -128.00 -45.43 -82.57 1 1.70e+01 3.46e-03 2.89e+01 dihedral pdb=" C4' DG M 13 " pdb=" C3' DG M 13 " pdb=" O3' DG M 13 " pdb=" P DT M 14 " ideal model delta sinusoidal sigma weight residual 220.00 51.81 168.19 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 11755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2635 0.075 - 0.149: 409 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.750 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 19386 Z= 0.349 Angle : 0.767 6.731 26403 Z= 0.512 Chirality : 0.051 0.373 3065 Planarity : 0.006 0.078 3163 Dihedral : 14.766 168.194 7516 Min Nonbonded Distance : 1.527 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.31 % Allowed : 0.46 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.17), residues: 2254 helix: 1.59 (0.17), residues: 893 sheet: 1.22 (0.23), residues: 465 loop : -1.03 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 13 TYR 0.107 0.005 TYR N 48 PHE 0.027 0.002 PHE H 22 TRP 0.007 0.001 TRP G 199 HIS 0.003 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.35 (19386) covalent geometry : angle 0.76657 / 0.51 (26403) hydrogen bonds : bond 0.14466 / 14.70 ( 798) hydrogen bonds : angle 6.06588 / 6.64 ( 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 : 0.714 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: 0.1688 time to fit residues: 76.4795 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 : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 117 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 295 ASN A 11 ASN A 154 GLN G 11 HIS E 27 HIS E 55 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.147185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.097323 restraints weight = 52258.617| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 4.30 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19386 Z= 0.140 Angle : 0.535 7.582 26403 Z= 0.298 Chirality : 0.044 0.269 3065 Planarity : 0.004 0.063 3163 Dihedral : 13.670 170.118 3210 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.70 % Allowed : 6.49 % Favored : 91.80 % 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: 1.18 (0.18), residues: 2254 helix: 2.24 (0.17), residues: 876 sheet: 1.25 (0.22), residues: 494 loop : -1.06 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 13 TYR 0.017 0.001 TYR G 215 PHE 0.021 0.001 PHE N 109 TRP 0.007 0.001 TRP G 199 HIS 0.004 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (19386) covalent geometry : angle 0.53464 / 0.30 (26403) hydrogen bonds : bond 0.06130 / 6.32 ( 798) hydrogen bonds : angle 4.22192 / 4.85 ( 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 146 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8142 (tmtt) REVERT: D 80 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8060 (tm-30) REVERT: D 91 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8411 (mppt) REVERT: A 124 MET cc_start: 0.8409 (tmm) cc_final: 0.8037 (tmm) REVERT: G 182 ARG cc_start: 0.7853 (pmt-80) cc_final: 0.7181 (ptt90) REVERT: E 78 GLN cc_start: 0.9047 (mp10) cc_final: 0.8818 (pm20) REVERT: E 150 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7991 (pp20) REVERT: E 227 TYR cc_start: 0.8028 (p90) cc_final: 0.7624 (p90) REVERT: E 245 MET cc_start: 0.5153 (mtt) cc_final: 0.3564 (ptt) REVERT: E 281 LYS cc_start: 0.9075 (tptp) cc_final: 0.8814 (ptmt) outliers start: 32 outliers final: 21 residues processed: 138 average time/residue: 0.1374 time to fit residues: 29.9481 Evaluate side-chains 119 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain K residue 128 MET Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 113 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 128 optimal weight: 2.9990 chunk 200 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS A 16 ASN E 27 HIS L 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.138524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.085197 restraints weight = 63109.416| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 5.37 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19386 Z= 0.257 Angle : 0.648 7.788 26403 Z= 0.355 Chirality : 0.046 0.172 3065 Planarity : 0.006 0.067 3163 Dihedral : 13.811 166.541 3210 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.86 % Allowed : 8.40 % Favored : 89.74 % 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 (0.17), residues: 2254 helix: 1.68 (0.17), residues: 886 sheet: 0.87 (0.23), residues: 473 loop : -1.40 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 28 TYR 0.019 0.002 TYR C 125 PHE 0.026 0.002 PHE C 159 TRP 0.010 0.002 TRP G 199 HIS 0.049 0.004 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.26 (19386) covalent geometry : angle 0.64768 / 0.35 (26403) hydrogen bonds : bond 0.05955 / 6.17 ( 798) hydrogen bonds : angle 4.31563 / 5.05 ( 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 139 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7102 (pp20) REVERT: C 96 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8497 (tmtt) REVERT: D 13 GLU cc_start: 0.6960 (tp30) cc_final: 0.6538 (tm-30) REVERT: D 91 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8223 (mppt) REVERT: D 112 MET cc_start: 0.8559 (mtp) cc_final: 0.8272 (mtp) REVERT: G 166 ARG cc_start: 0.9072 (mtp-110) cc_final: 0.8860 (mtp-110) REVERT: E 27 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6814 (m-70) REVERT: E 78 GLN cc_start: 0.9025 (mp10) cc_final: 0.8761 (pm20) REVERT: E 150 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8033 (pp20) REVERT: E 227 TYR cc_start: 0.8362 (p90) cc_final: 0.7889 (p90) REVERT: E 245 MET cc_start: 0.5178 (mtt) cc_final: 0.4222 (ptt) REVERT: E 281 LYS cc_start: 0.9098 (tptp) cc_final: 0.8803 (ptmt) outliers start: 35 outliers final: 25 residues processed: 130 average time/residue: 0.1553 time to fit residues: 31.0337 Evaluate side-chains 123 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain K residue 128 MET Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 58 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 24 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 41 optimal weight: 0.7980 chunk 200 optimal weight: 0.4980 chunk 206 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 189 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 295 ASN A 16 ASN E 27 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.141146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.088961 restraints weight = 43628.580| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.95 r_work: 0.3386 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19386 Z= 0.108 Angle : 0.479 8.199 26403 Z= 0.265 Chirality : 0.042 0.196 3065 Planarity : 0.004 0.053 3163 Dihedral : 13.573 165.669 3209 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.39 % Allowed : 8.97 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.17), residues: 2254 helix: 2.01 (0.17), residues: 887 sheet: 0.95 (0.23), residues: 474 loop : -1.26 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 28 TYR 0.014 0.001 TYR G 215 PHE 0.015 0.001 PHE C 159 TRP 0.007 0.002 TRP G 192 HIS 0.013 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (19386) covalent geometry : angle 0.47924 / 0.26 (26403) hydrogen bonds : bond 0.04412 / 4.55 ( 798) hydrogen bonds : angle 3.83582 / 4.40 ( 2280) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8435 (tmtt) REVERT: D 80 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8285 (tm-30) REVERT: D 91 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8379 (mppt) REVERT: A 1 MET cc_start: 0.8291 (ttp) cc_final: 0.8024 (ttp) REVERT: A 124 MET cc_start: 0.8735 (tmm) cc_final: 0.8464 (tmm) REVERT: G 182 ARG cc_start: 0.7684 (pmt-80) cc_final: 0.7275 (ppt90) REVERT: E 78 GLN cc_start: 0.9160 (mp10) cc_final: 0.8760 (pm20) REVERT: E 124 MET cc_start: 0.8172 (ttt) cc_final: 0.7936 (ttt) REVERT: E 150 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7978 (pp20) REVERT: E 227 TYR cc_start: 0.8218 (p90) cc_final: 0.7827 (p90) REVERT: E 245 MET cc_start: 0.5159 (mtt) cc_final: 0.3406 (ptt) REVERT: E 281 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8873 (ptmt) REVERT: L 112 MET cc_start: -0.1615 (ptt) cc_final: -0.2119 (ttp) outliers start: 26 outliers final: 15 residues processed: 118 average time/residue: 0.1547 time to fit residues: 28.6669 Evaluate side-chains 112 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain K residue 128 MET Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 58 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 106 optimal weight: 0.0770 chunk 216 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 152 optimal weight: 0.1980 chunk 206 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.139903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.086292 restraints weight = 62728.887| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 5.07 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3407 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= 0.129 Angle : 0.495 11.925 26403 Z= 0.266 Chirality : 0.042 0.196 3065 Planarity : 0.004 0.048 3163 Dihedral : 13.403 164.631 3209 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.49 % Allowed : 9.59 % Favored : 88.92 % 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: 0.90 (0.18), residues: 2254 helix: 2.15 (0.17), residues: 887 sheet: 0.81 (0.23), residues: 490 loop : -1.21 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 166 TYR 0.018 0.001 TYR E 227 PHE 0.015 0.001 PHE C 159 TRP 0.008 0.001 TRP G 192 HIS 0.006 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (19386) covalent geometry : angle 0.49509 / 0.27 (26403) hydrogen bonds : bond 0.04186 / 4.29 ( 798) hydrogen bonds : angle 3.76592 / 4.33 ( 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 131 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8536 (tmtt) REVERT: C 124 MET cc_start: 0.7588 (ttt) cc_final: 0.7287 (ttt) REVERT: D 13 GLU cc_start: 0.6545 (tp30) cc_final: 0.6200 (tm-30) REVERT: D 15 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6062 (mp) REVERT: D 80 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8078 (tm-30) REVERT: D 91 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8185 (mppt) REVERT: A 124 MET cc_start: 0.8328 (tmm) cc_final: 0.7997 (tmm) REVERT: G 182 ARG cc_start: 0.7624 (pmt-80) cc_final: 0.7248 (ppt90) REVERT: E 78 GLN cc_start: 0.9103 (mp10) cc_final: 0.8833 (pm20) REVERT: E 150 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7970 (pp20) REVERT: E 227 TYR cc_start: 0.8413 (p90) cc_final: 0.8001 (p90) REVERT: E 245 MET cc_start: 0.5322 (mtt) cc_final: 0.3802 (ptt) REVERT: E 281 LYS cc_start: 0.9011 (tptp) cc_final: 0.8756 (ptmt) outliers start: 28 outliers final: 18 residues processed: 122 average time/residue: 0.1442 time to fit residues: 27.9604 Evaluate side-chains 113 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 C residue 1 MET Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 113 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 215 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 213 optimal weight: 0.0010 chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 196 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 140 GLN ** 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 = 0.4390 r_free = 0.4390 target = 0.139422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.086630 restraints weight = 58958.965| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 4.91 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3600 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= 0.127 Angle : 0.485 8.292 26403 Z= 0.261 Chirality : 0.042 0.189 3065 Planarity : 0.004 0.047 3163 Dihedral : 13.321 164.025 3209 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.49 % Allowed : 10.15 % Favored : 88.35 % 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: 0.95 (0.18), residues: 2254 helix: 2.20 (0.17), residues: 886 sheet: 0.80 (0.23), residues: 486 loop : -1.16 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 166 TYR 0.018 0.001 TYR E 227 PHE 0.016 0.001 PHE C 159 TRP 0.008 0.001 TRP G 192 HIS 0.006 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (19386) covalent geometry : angle 0.48488 / 0.26 (26403) hydrogen bonds : bond 0.04061 / 4.14 ( 798) hydrogen bonds : angle 3.71980 / 4.28 ( 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 122 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6830 (tm-30) REVERT: C 96 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8651 (tmtt) REVERT: C 178 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8193 (mt-10) REVERT: D 91 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8154 (mppt) REVERT: A 1 MET cc_start: 0.8362 (ttp) cc_final: 0.7889 (ttp) REVERT: A 124 MET cc_start: 0.8333 (tmm) cc_final: 0.7994 (tmm) REVERT: G 182 ARG cc_start: 0.7610 (pmt-80) cc_final: 0.7315 (ppt90) REVERT: E 78 GLN cc_start: 0.9094 (mp10) cc_final: 0.8850 (pm20) REVERT: E 150 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7995 (pp20) REVERT: E 227 TYR cc_start: 0.8521 (p90) cc_final: 0.8148 (p90) REVERT: E 245 MET cc_start: 0.5998 (mtt) cc_final: 0.4694 (ptt) REVERT: E 281 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8707 (ptmt) REVERT: N 112 MET cc_start: 0.5851 (tmm) cc_final: 0.5496 (ptm) outliers start: 28 outliers final: 20 residues processed: 115 average time/residue: 0.1333 time to fit residues: 24.9722 Evaluate side-chains 116 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU 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 C residue 1 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain N residue 53 ILE 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: 6.9990 chunk 195 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 170 optimal weight: 0.0060 chunk 164 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.136551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.083515 restraints weight = 63309.199| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 6.01 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4002 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= 0.200 Angle : 0.549 11.729 26403 Z= 0.297 Chirality : 0.043 0.212 3065 Planarity : 0.004 0.047 3163 Dihedral : 13.309 162.431 3209 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.55 % Allowed : 10.67 % Favored : 87.78 % 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 (0.18), residues: 2254 helix: 2.07 (0.17), residues: 882 sheet: 0.70 (0.23), residues: 480 loop : -1.26 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 166 TYR 0.023 0.001 TYR L 119 PHE 0.024 0.002 PHE E 123 TRP 0.012 0.002 TRP G 192 HIS 0.010 0.002 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (19386) covalent geometry : angle 0.54896 / 0.30 (26403) hydrogen bonds : bond 0.04755 / 4.85 ( 798) hydrogen bonds : angle 3.89799 / 4.56 ( 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 128 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6891 (tm-30) REVERT: C 13 GLU cc_start: 0.7315 (tm-30) cc_final: 0.7074 (pp20) REVERT: C 96 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8617 (tptm) REVERT: C 124 MET cc_start: 0.7791 (ttt) cc_final: 0.7382 (ttt) REVERT: D 91 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8115 (mppt) REVERT: A 1 MET cc_start: 0.8437 (ttp) cc_final: 0.7939 (ttp) REVERT: A 124 MET cc_start: 0.8396 (tmm) cc_final: 0.8032 (tmm) REVERT: E 78 GLN cc_start: 0.9100 (mp10) cc_final: 0.8874 (pm20) REVERT: E 281 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8674 (ptmt) outliers start: 29 outliers final: 23 residues processed: 121 average time/residue: 0.1316 time to fit residues: 25.5454 Evaluate side-chains 115 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain L residue 128 MET 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: 30.0000 chunk 162 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 202 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 143 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 83 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.138025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.086019 restraints weight = 62376.402| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 4.92 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 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 = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4087 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= 0.119 Angle : 0.487 8.968 26403 Z= 0.264 Chirality : 0.042 0.204 3065 Planarity : 0.003 0.042 3163 Dihedral : 13.257 163.206 3209 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.44 % Allowed : 11.13 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2254 helix: 2.24 (0.17), residues: 880 sheet: 0.65 (0.23), residues: 484 loop : -1.21 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 166 TYR 0.020 0.001 TYR E 227 PHE 0.015 0.001 PHE C 159 TRP 0.009 0.001 TRP G 192 HIS 0.005 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (19386) covalent geometry : angle 0.48699 / 0.26 (26403) hydrogen bonds : bond 0.04054 / 4.11 ( 798) hydrogen bonds : angle 3.72974 / 4.31 ( 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 117 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6560 (tp30) REVERT: B 96 LYS cc_start: 0.8614 (mmmm) cc_final: 0.8341 (tppp) REVERT: C 13 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.7025 (pp20) REVERT: C 21 ILE cc_start: 0.8401 (mt) cc_final: 0.8149 (mm) REVERT: C 96 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8612 (tptm) REVERT: C 124 MET cc_start: 0.7748 (ttt) cc_final: 0.7470 (ttt) REVERT: D 91 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8082 (mppt) REVERT: A 1 MET cc_start: 0.8408 (ttp) cc_final: 0.7854 (ttp) REVERT: A 124 MET cc_start: 0.8371 (tmm) cc_final: 0.8029 (tmm) REVERT: G 182 ARG cc_start: 0.7633 (pmt-80) cc_final: 0.7426 (ppt90) REVERT: E 78 GLN cc_start: 0.9078 (mp10) cc_final: 0.8826 (pm20) REVERT: E 124 MET cc_start: 0.7091 (ttt) cc_final: 0.6356 (ttt) REVERT: E 227 TYR cc_start: 0.8514 (p90) cc_final: 0.8148 (p90) REVERT: E 245 MET cc_start: 0.3324 (ptt) cc_final: 0.3121 (ptt) REVERT: E 281 LYS cc_start: 0.8881 (tptp) cc_final: 0.8648 (ptmt) REVERT: N 112 MET cc_start: 0.6382 (tmm) cc_final: 0.6136 (ptm) outliers start: 27 outliers final: 19 residues processed: 113 average time/residue: 0.1377 time to fit residues: 25.2024 Evaluate side-chains 111 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU 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 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 251 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain L residue 128 MET Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 53 ILE 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: 5.9990 chunk 61 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.137133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.084372 restraints weight = 43475.120| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 4.36 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19386 Z= 0.150 Angle : 0.506 9.236 26403 Z= 0.272 Chirality : 0.042 0.219 3065 Planarity : 0.004 0.047 3163 Dihedral : 13.189 163.179 3209 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.70 % Allowed : 10.88 % Favored : 87.42 % 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: 0.86 (0.18), residues: 2254 helix: 2.21 (0.17), residues: 880 sheet: 0.68 (0.23), residues: 476 loop : -1.21 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 166 TYR 0.021 0.001 TYR E 227 PHE 0.017 0.001 PHE C 159 TRP 0.010 0.001 TRP G 192 HIS 0.007 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (19386) covalent geometry : angle 0.50601 / 0.27 (26403) hydrogen bonds : bond 0.04181 / 4.23 ( 798) hydrogen bonds : angle 3.76003 / 4.38 ( 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 126 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: B 13 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6554 (tp30) REVERT: C 13 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7116 (pp20) REVERT: C 21 ILE cc_start: 0.8357 (mt) cc_final: 0.8125 (mm) REVERT: C 96 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8717 (tmtt) REVERT: C 124 MET cc_start: 0.7758 (ttt) cc_final: 0.7525 (ttt) REVERT: D 91 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8112 (mppt) REVERT: A 124 MET cc_start: 0.8388 (tmm) cc_final: 0.8045 (tmm) REVERT: G 182 ARG cc_start: 0.7682 (pmt-80) cc_final: 0.7429 (ppt90) REVERT: E 78 GLN cc_start: 0.9098 (mp10) cc_final: 0.8854 (pm20) REVERT: E 112 MET cc_start: 0.9087 (mtm) cc_final: 0.8815 (mpp) REVERT: E 124 MET cc_start: 0.7272 (ttt) cc_final: 0.6530 (ttt) REVERT: E 227 TYR cc_start: 0.8647 (p90) cc_final: 0.8224 (p90) REVERT: E 245 MET cc_start: 0.3567 (ptt) cc_final: 0.3354 (ptt) REVERT: E 281 LYS cc_start: 0.8997 (tptp) cc_final: 0.8643 (ptmt) REVERT: N 112 MET cc_start: 0.5853 (tmm) cc_final: 0.5634 (ptm) outliers start: 32 outliers final: 24 residues processed: 120 average time/residue: 0.1194 time to fit residues: 23.2612 Evaluate side-chains 117 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU 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 142 MET 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 305 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 15 LEU 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 266 ASP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain L residue 128 MET 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: 5.9990 chunk 126 optimal weight: 0.0570 chunk 228 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 189 optimal weight: 9.9990 chunk 124 optimal weight: 0.0970 chunk 224 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.139231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.088483 restraints weight = 51330.000| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 4.35 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19386 Z= 0.094 Angle : 0.479 13.122 26403 Z= 0.253 Chirality : 0.041 0.203 3065 Planarity : 0.003 0.038 3163 Dihedral : 13.097 164.287 3209 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.08 % Allowed : 11.49 % Favored : 87.42 % 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: 2.37 (0.17), residues: 880 sheet: 0.80 (0.24), residues: 470 loop : -1.04 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 166 TYR 0.021 0.001 TYR E 227 PHE 0.012 0.001 PHE C 159 TRP 0.009 0.001 TRP G 12 HIS 0.003 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (19386) covalent geometry : angle 0.47886 / 0.25 (26403) hydrogen bonds : bond 0.03537 / 3.56 ( 798) hydrogen bonds : angle 3.56257 / 4.12 ( 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 118 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: B 96 LYS cc_start: 0.8555 (mmmm) cc_final: 0.8315 (tppp) REVERT: C 13 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7105 (pp20) REVERT: C 21 ILE cc_start: 0.8323 (mt) cc_final: 0.8089 (mm) REVERT: C 96 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8657 (tptm) REVERT: C 112 MET cc_start: 0.8072 (mtp) cc_final: 0.7855 (mtp) REVERT: C 124 MET cc_start: 0.7623 (ttt) cc_final: 0.7416 (ttt) REVERT: D 80 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8127 (tm-30) REVERT: D 91 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8128 (mppt) REVERT: A 1 MET cc_start: 0.8331 (ttp) cc_final: 0.7816 (ttp) REVERT: A 124 MET cc_start: 0.8337 (tmm) cc_final: 0.8034 (tmm) REVERT: E 78 GLN cc_start: 0.9080 (mp10) cc_final: 0.8821 (pm20) REVERT: E 124 MET cc_start: 0.7212 (ttt) cc_final: 0.6505 (ttt) REVERT: E 227 TYR cc_start: 0.8396 (p90) cc_final: 0.8035 (p90) REVERT: E 245 MET cc_start: 0.2983 (ptt) cc_final: 0.2651 (ptt) REVERT: E 281 LYS cc_start: 0.8862 (tptp) cc_final: 0.8550 (ptmt) REVERT: N 112 MET cc_start: 0.6110 (tmm) cc_final: 0.5859 (ptm) outliers start: 20 outliers final: 17 residues processed: 113 average time/residue: 0.1357 time to fit residues: 24.4248 Evaluate side-chains 111 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 91 LYS 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 217 LEU Chi-restraints excluded: chain L residue 128 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 14 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 218 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.138813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.088178 restraints weight = 48765.855| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 4.04 r_work: 0.3366 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19386 Z= 0.104 Angle : 0.486 10.810 26403 Z= 0.255 Chirality : 0.041 0.214 3065 Planarity : 0.003 0.038 3163 Dihedral : 13.062 164.662 3209 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.24 % Allowed : 11.75 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 2254 helix: 2.39 (0.17), residues: 882 sheet: 0.74 (0.23), residues: 484 loop : -1.04 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 166 TYR 0.022 0.001 TYR E 227 PHE 0.012 0.001 PHE C 159 TRP 0.007 0.001 TRP G 192 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (19386) covalent geometry : angle 0.48638 / 0.25 (26403) hydrogen bonds : bond 0.03550 / 3.57 ( 798) hydrogen bonds : angle 3.56537 / 4.18 ( 2280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8468.46 seconds wall clock time: 144 minutes 34.42 seconds (8674.42 seconds total)