Starting phenix.real_space_refine on Sun Aug 9 14:30:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cp1_45796/08_2026/9cp1_45796_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cp1_45796/08_2026/9cp1_45796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cp1_45796/08_2026/9cp1_45796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cp1_45796/08_2026/9cp1_45796.map" model { file = "/net/cci-nas-00/data/ceres_data/9cp1_45796/08_2026/9cp1_45796_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cp1_45796/08_2026/9cp1_45796_trim.cif" } resolution = 2.97 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= 0.027 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 510 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 S 53 5.16 5 C 10719 2.51 5 N 2832 2.21 5 O 3367 1.98 5 H 16838 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33857 Number of models: 1 Model: "" Number of chains: 15 Chain: "F" Number of atoms: 3989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 3989 Classifications: {'peptide': 252} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain breaks: 4 Chain: "B" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4974 Classifications: {'peptide': 317} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "C" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4974 Classifications: {'peptide': 317} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "E" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4974 Classifications: {'peptide': 317} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "D" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4974 Classifications: {'peptide': 317} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "A" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 4974 Classifications: {'peptide': 317} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "G" Number of atoms: 3391 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 3380 Classifications: {'peptide': 211} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 211, 3380 Classifications: {'peptide': 211} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 bond proxies already assigned to first conformer: 3409 Chain: "S" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 1209 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 13, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 19, 'rna3p': 18} Chain: "M" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 350 Classifications: {'DNA': 11} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 10} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "B" 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: "E" 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} Time building chain proxies: 6.39, per 1000 atoms: 0.19 Number of scatterers: 33857 At special positions: 0 Unit cell: (100.82, 129.22, 178.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 53 16.00 P 48 15.00 O 3367 8.00 N 2832 7.00 C 10719 6.00 H 16838 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 993.1 milliseconds 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3774 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 25 sheets defined 34.8% alpha, 16.6% beta 5 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 5.55 Creating SS restraints... Processing helix chain 'F' and resid 49 through 69 removed outlier: 4.214A pdb=" N LEU F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 78 removed outlier: 4.094A pdb=" N GLN F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 94 Processing helix chain 'F' and resid 100 through 102 No H-bonds generated for 'chain 'F' and resid 100 through 102' Processing helix chain 'F' and resid 103 through 115 Processing helix chain 'F' and resid 116 through 121 Processing helix chain 'F' and resid 192 through 195 Processing helix chain 'F' and resid 207 through 232 removed outlier: 4.765A pdb=" N ALA F 216 " --> pdb=" O GLU F 212 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LYS F 217 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER F 228 " --> pdb=" O LYS F 224 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 285 removed outlier: 3.539A pdb=" N ASN F 285 " --> pdb=" O LYS F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 320 Processing helix chain 'B' and resid 49 through 69 removed outlier: 4.151A pdb=" N LEU B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 removed outlier: 4.050A pdb=" N GLN B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.572A pdb=" N LEU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 115 through 122 Processing helix chain 'B' and resid 192 through 195 removed outlier: 3.661A 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: 3.606A pdb=" N LEU B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 4.394A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.585A pdb=" N ASN B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.948A pdb=" N LEU B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 69 removed outlier: 4.323A pdb=" N LEU C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.750A pdb=" N GLN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.560A 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 Processing helix chain 'C' and resid 192 through 195 removed outlier: 3.673A 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: 3.720A pdb=" N LEU C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ALA C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYS C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 4.363A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.521A pdb=" N ASN C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.973A pdb=" N LEU C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 69 removed outlier: 4.280A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 removed outlier: 3.905A 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 100 through 102 No H-bonds generated for 'chain 'E' and resid 100 through 102' Processing helix chain 'E' and resid 103 through 113 Processing helix chain 'E' and resid 115 through 122 removed outlier: 3.533A pdb=" N ASP E 119 " --> pdb=" O ASP E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 195 removed outlier: 3.606A pdb=" N ILE E 195 " --> pdb=" O GLU E 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 192 through 195' Processing helix chain 'E' and resid 207 through 225 removed outlier: 3.537A pdb=" N LEU E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LYS E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 232 removed outlier: 4.303A pdb=" N LEU E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 284 Processing helix chain 'E' and resid 310 through 321 removed outlier: 3.961A pdb=" N LEU E 314 " --> pdb=" O THR E 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: 3.927A pdb=" N GLN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.531A 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 121 Processing helix chain 'D' and resid 207 through 232 removed outlier: 3.672A pdb=" N LEU D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LYS D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 285 removed outlier: 3.559A pdb=" N ASN D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 321 removed outlier: 4.002A pdb=" N LEU D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 69 removed outlier: 4.484A pdb=" N LEU A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.775A pdb=" N GLN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.522A pdb=" N ILE A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.519A 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: 3.613A pdb=" N ASP A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 195 removed outlier: 3.582A pdb=" N ILE A 195 " --> pdb=" O GLU A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 195' Processing helix chain 'A' and resid 207 through 225 removed outlier: 3.797A pdb=" N LEU A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ALA A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LYS A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 4.123A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.793A pdb=" N THR A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.903A 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: 3.772A pdb=" N ILE G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 137 through 139 removed outlier: 3.637A pdb=" N SER F 249 " --> pdb=" O ARG F 7 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU F 9 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU F 247 " --> pdb=" O LEU F 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 29 through 36 Processing sheet with id=AA3, first strand: chain 'F' and resid 123 through 125 Processing sheet with id=AA4, 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: 4.063A pdb=" N THR B 306 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 123 through 125 Processing sheet with id=AA7, 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 24 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 24 through 27 current: chain 'C' and resid 174 through 182 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 174 through 182 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=AA8, first strand: chain 'C' and resid 29 through 36 Processing sheet with id=AA9, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AB1, 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 174 through 182 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 174 through 182 current: chain 'E' and resid 289 through 295 removed outlier: 4.558A pdb=" N THR E 306 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 29 through 36 Processing sheet with id=AB3, first strand: chain 'E' and resid 123 through 125 Processing sheet with id=AB4, 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 182 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 174 through 182 current: chain 'D' and resid 289 through 295 removed outlier: 4.270A pdb=" N THR D 306 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 29 through 36 Processing sheet with id=AB6, first strand: chain 'D' and resid 123 through 125 Processing sheet with id=AB7, first strand: chain 'A' and resid 2 through 8 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2 through 8 current: chain 'A' and resid 184 through 190 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 190 current: chain 'A' and resid 289 through 295 removed outlier: 3.612A pdb=" N THR A 306 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 10 through 13 current: chain 'A' and resid 174 through 182 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AC1, first strand: chain 'A' and resid 124 through 125 removed outlier: 3.506A pdb=" N VAL A 131 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 68 through 73 removed outlier: 3.871A pdb=" N ASN G 154 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS G 9 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL G 152 " --> pdb=" O LYS G 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 13 through 14 removed outlier: 3.611A pdb=" N PHE G 14 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 161 through 163 removed outlier: 3.692A pdb=" N LYS G 161 " --> pdb=" O GLU G 231 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER G 240 " --> pdb=" O GLU G 228 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR G 230 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL G 238 " --> pdb=" O TYR G 230 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AC6, first strand: chain 'G' and resid 173 through 174 Processing sheet with id=AC7, first strand: chain 'G' and resid 212 through 213 removed outlier: 3.793A pdb=" N ALA G 218 " --> pdb=" O THR G 213 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 7.74 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.37: 22260 1.37 - 1.89: 11985 1.89 - 2.42: 0 2.42 - 2.95: 0 2.95 - 3.48: 1 Bond restraints: 34246 Sorted by residual: bond pdb=" C5' C S 28 " pdb=" H5' C S 28 " ideal model delta sigma weight residual 0.970 3.478 -2.508 2.00e-02 2.50e+03 1.57e+04 bond pdb=" N4 C S 28 " pdb=" H42 C S 28 " ideal model delta sigma weight residual 0.860 1.014 -0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" C6 C S 28 " pdb=" H6 C S 28 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C1' C S 28 " pdb=" H1' C S 28 " ideal model delta sigma weight residual 0.970 1.112 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C4' C S 28 " pdb=" H4' C S 28 " ideal model delta sigma weight residual 0.970 1.111 -0.141 2.00e-02 2.50e+03 5.00e+01 ... (remaining 34241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.56: 62145 9.56 - 19.12: 2 19.12 - 28.68: 1 28.68 - 38.23: 0 38.23 - 47.79: 1 Bond angle restraints: 62149 Sorted by residual: angle pdb=" H5' C S 28 " pdb=" C5' C S 28 " pdb="H5'' C S 28 " ideal model delta sigma weight residual 109.00 61.21 47.79 3.00e+00 1.11e-01 2.54e+02 angle pdb=" O5' C S 28 " pdb=" C5' C S 28 " pdb=" H5' C S 28 " ideal model delta sigma weight residual 109.00 136.20 -27.20 3.00e+00 1.11e-01 8.22e+01 angle pdb=" N ILE F 82 " pdb=" CA ILE F 82 " pdb=" C ILE F 82 " ideal model delta sigma weight residual 112.96 107.96 5.00 1.00e+00 1.00e+00 2.50e+01 angle pdb=" C1' U S 32 " pdb=" N1 U S 32 " pdb=" C2 U S 32 " ideal model delta sigma weight residual 117.70 123.57 -5.87 1.20e+00 6.94e-01 2.39e+01 angle pdb=" N3 DT M 17 " pdb=" C4 DT M 17 " pdb=" O4 DT M 17 " ideal model delta sigma weight residual 119.90 122.75 -2.85 6.00e-01 2.78e+00 2.26e+01 ... (remaining 62144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 15362 36.00 - 71.99: 541 71.99 - 107.99: 38 107.99 - 143.98: 1 143.98 - 179.98: 9 Dihedral angle restraints: 15951 sinusoidal: 9164 harmonic: 6787 Sorted by residual: dihedral pdb=" O4' U S 38 " pdb=" C1' U S 38 " pdb=" N1 U S 38 " pdb=" C2 U S 38 " ideal model delta sinusoidal sigma weight residual 232.00 55.67 176.33 1 1.70e+01 3.46e-03 6.64e+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 -34.96 -93.04 1 1.70e+01 3.46e-03 3.50e+01 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 232.00 158.70 73.30 1 1.70e+01 3.46e-03 2.37e+01 ... (remaining 15948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2097 0.048 - 0.095: 437 0.095 - 0.143: 189 0.143 - 0.190: 5 0.190 - 0.238: 8 Chirality restraints: 2736 Sorted by residual: chirality pdb=" CB VAL A 18 " pdb=" CA VAL A 18 " pdb=" CG1 VAL A 18 " pdb=" CG2 VAL A 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL B 18 " pdb=" CA VAL B 18 " pdb=" CG1 VAL B 18 " pdb=" CG2 VAL B 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL D 18 " pdb=" CA VAL D 18 " pdb=" CG1 VAL D 18 " pdb=" CG2 VAL D 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2733 not shown) Planarity restraints: 4817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A S 24 " -0.027 2.00e-02 2.50e+03 1.28e-02 5.34e+00 pdb=" N9 A S 24 " 0.034 2.00e-02 2.50e+03 pdb=" C8 A S 24 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A S 24 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A S 24 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A S 24 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A S 24 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A S 24 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A S 24 " -0.000 2.00e-02 2.50e+03 pdb=" N3 A S 24 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A S 24 " 0.006 2.00e-02 2.50e+03 pdb=" H8 A S 24 " -0.010 2.00e-02 2.50e+03 pdb=" H2 A S 24 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 30 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO E 31 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 31 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 31 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A S 36 " -0.019 2.00e-02 2.50e+03 9.30e-03 2.81e+00 pdb=" N9 A S 36 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A S 36 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A S 36 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A S 36 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A S 36 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A S 36 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A S 36 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A S 36 " -0.000 2.00e-02 2.50e+03 pdb=" N3 A S 36 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A S 36 " 0.002 2.00e-02 2.50e+03 pdb=" H8 A S 36 " -0.008 2.00e-02 2.50e+03 pdb=" H2 A S 36 " -0.000 2.00e-02 2.50e+03 ... (remaining 4814 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 525 2.07 - 2.70: 53723 2.70 - 3.33: 89763 3.33 - 3.97: 117641 3.97 - 4.60: 188560 Nonbonded interactions: 450212 Sorted by model distance: nonbonded pdb=" OH TYR A 141 " pdb=" HZ3 LYS G 111 " model vdw 1.437 2.450 nonbonded pdb=" OE1 GLU E 108 " pdb=" HG1 THR E 200 " model vdw 1.480 2.450 nonbonded pdb=" H1 G S 29 " pdb=" H42 DC M 10 " model vdw 1.501 2.100 nonbonded pdb=" HD1 HIS F 55 " pdb=" OP2 U S 38 " model vdw 1.505 2.450 nonbonded pdb=" OE1 GLU D 108 " pdb=" HG1 THR D 200 " model vdw 1.518 2.450 ... (remaining 450207 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.080 Construct map_model_manager: 0.210 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 36.430 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17409 Z= 0.189 Angle : 0.546 8.970 23708 Z= 0.352 Chirality : 0.046 0.238 2736 Planarity : 0.004 0.043 2838 Dihedral : 15.342 176.332 6792 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.12 % Allowed : 0.12 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.54 (0.19), residues: 2013 helix: 1.55 (0.21), residues: 635 sheet: 1.34 (0.23), residues: 439 loop : -1.00 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 132 TYR 0.009 0.001 TYR D 79 PHE 0.019 0.001 PHE A 186 TRP 0.008 0.001 TRP G 12 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.19 (17408) covalent geometry : angle 0.54580 / 0.35 (23708) hydrogen bonds : bond 0.13554 / 9.06 ( 549) hydrogen bonds : angle 5.36922 / 3.74 ( 1551) Misc. bond : bond 0.00070 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 GLN cc_start: 0.8640 (mp10) cc_final: 0.8286 (pm20) REVERT: F 86 THR cc_start: 0.8233 (p) cc_final: 0.7970 (t) REVERT: F 132 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7623 (mtm-85) REVERT: F 213 ARG cc_start: 0.8969 (mtt180) cc_final: 0.8652 (tpm170) REVERT: F 248 MET cc_start: 0.5400 (mmm) cc_final: 0.5030 (mmp) REVERT: F 260 MET cc_start: 0.7836 (mtm) cc_final: 0.7330 (ptm) REVERT: F 266 ASP cc_start: 0.8530 (m-30) cc_final: 0.8170 (p0) REVERT: B 13 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6822 (pp20) REVERT: B 151 ILE cc_start: 0.9142 (mt) cc_final: 0.8832 (OUTLIER) REVERT: C 191 ASP cc_start: 0.8299 (p0) cc_final: 0.8044 (p0) REVERT: E 124 MET cc_start: 0.8953 (ttp) cc_final: 0.8727 (ttp) REVERT: E 193 ASP cc_start: 0.8566 (m-30) cc_final: 0.8215 (m-30) REVERT: E 293 VAL cc_start: 0.8768 (t) cc_final: 0.8559 (p) REVERT: E 319 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7938 (mt-10) REVERT: D 13 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7446 (pp20) REVERT: D 163 PHE cc_start: 0.9016 (t80) cc_final: 0.8716 (t80) REVERT: D 260 MET cc_start: 0.8472 (mtm) cc_final: 0.7958 (mmt) REVERT: A 96 LYS cc_start: 0.9250 (mmtt) cc_final: 0.8993 (tttm) REVERT: A 124 MET cc_start: 0.8851 (ttp) cc_final: 0.8437 (ttm) REVERT: A 142 MET cc_start: 0.9083 (ttm) cc_final: 0.8724 (ttt) REVERT: A 143 ILE cc_start: 0.8950 (mt) cc_final: 0.8710 (pt) outliers start: 1 outliers final: 4 residues processed: 252 average time/residue: 1.4303 time to fit residues: 402.6978 Evaluate side-chains 129 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain C residue 143 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.100675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.070228 restraints weight = 106640.730| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.96 r_work: 0.2982 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17409 Z= 0.176 Angle : 0.562 6.870 23708 Z= 0.299 Chirality : 0.044 0.228 2736 Planarity : 0.005 0.079 2838 Dihedral : 14.346 177.046 2918 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.92 % Allowed : 8.75 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.36 (0.18), residues: 2013 helix: 1.47 (0.21), residues: 643 sheet: 1.05 (0.23), residues: 435 loop : -1.06 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 174 TYR 0.009 0.001 TYR A 141 PHE 0.018 0.001 PHE C 159 TRP 0.006 0.001 TRP G 12 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (17408) covalent geometry : angle 0.56223 / 0.30 (23708) hydrogen bonds : bond 0.05582 / 3.71 ( 549) hydrogen bonds : angle 4.49065 / 3.06 ( 1551) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 GLN cc_start: 0.8716 (mp10) cc_final: 0.8477 (mp10) REVERT: F 248 MET cc_start: 0.5791 (mmm) cc_final: 0.5439 (mmp) REVERT: F 266 ASP cc_start: 0.8581 (m-30) cc_final: 0.8290 (p0) REVERT: F 317 LYS cc_start: 0.9012 (mttt) cc_final: 0.8750 (tptp) REVERT: B 13 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7345 (pp20) REVERT: B 151 ILE cc_start: 0.9198 (mt) cc_final: 0.8994 (OUTLIER) REVERT: C 13 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7472 (pp20) REVERT: C 191 ASP cc_start: 0.8389 (p0) cc_final: 0.8185 (p0) REVERT: E 13 GLU cc_start: 0.6911 (tm-30) cc_final: 0.6596 (pp20) REVERT: E 193 ASP cc_start: 0.8599 (m-30) cc_final: 0.8247 (m-30) REVERT: E 293 VAL cc_start: 0.8552 (t) cc_final: 0.8112 (p) REVERT: E 319 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7799 (mt-10) REVERT: D 13 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7710 (pp20) REVERT: D 163 PHE cc_start: 0.9134 (t80) cc_final: 0.8923 (t80) REVERT: D 260 MET cc_start: 0.8641 (mtm) cc_final: 0.8171 (mmt) REVERT: A 96 LYS cc_start: 0.9221 (mmtt) cc_final: 0.9013 (tttm) REVERT: A 124 MET cc_start: 0.9030 (ttp) cc_final: 0.8649 (ttm) outliers start: 15 outliers final: 9 residues processed: 138 average time/residue: 1.4164 time to fit residues: 218.7226 Evaluate side-chains 117 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 276 ARG Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 147 optimal weight: 0.0980 chunk 65 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 58 GLN B 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.100482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.069961 restraints weight = 112182.683| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.02 r_work: 0.2976 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17409 Z= 0.153 Angle : 0.518 7.388 23708 Z= 0.276 Chirality : 0.043 0.233 2736 Planarity : 0.004 0.041 2838 Dihedral : 14.300 177.717 2916 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.69 % Allowed : 10.19 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.22 (0.18), residues: 2013 helix: 1.46 (0.21), residues: 643 sheet: 0.79 (0.23), residues: 435 loop : -1.14 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 133 TYR 0.009 0.001 TYR F 57 PHE 0.013 0.001 PHE C 159 TRP 0.006 0.001 TRP G 12 HIS 0.002 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (17408) covalent geometry : angle 0.51810 / 0.28 (23708) hydrogen bonds : bond 0.04880 / 3.26 ( 549) hydrogen bonds : angle 4.31046 / 2.93 ( 1551) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 GLN cc_start: 0.8726 (mp10) cc_final: 0.8487 (mp10) REVERT: F 124 MET cc_start: 0.8060 (ttt) cc_final: 0.7634 (ttt) REVERT: F 248 MET cc_start: 0.5823 (mmm) cc_final: 0.5468 (mmp) REVERT: F 266 ASP cc_start: 0.8585 (m-30) cc_final: 0.8279 (p0) REVERT: F 269 TYR cc_start: 0.7907 (p90) cc_final: 0.7510 (p90) REVERT: F 308 LEU cc_start: 0.4748 (OUTLIER) cc_final: 0.4326 (mp) REVERT: F 317 LYS cc_start: 0.9045 (mttt) cc_final: 0.8741 (tptp) REVERT: B 13 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7430 (pp20) REVERT: C 13 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7593 (pp20) REVERT: C 191 ASP cc_start: 0.8420 (p0) cc_final: 0.8203 (p0) REVERT: E 13 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6876 (pp20) REVERT: E 160 HIS cc_start: 0.6792 (m-70) cc_final: 0.6527 (m-70) REVERT: E 193 ASP cc_start: 0.8692 (m-30) cc_final: 0.8341 (m-30) REVERT: E 301 VAL cc_start: 0.8949 (p) cc_final: 0.8635 (m) REVERT: E 319 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7808 (mt-10) REVERT: D 13 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7781 (pp20) REVERT: D 260 MET cc_start: 0.8682 (mtm) cc_final: 0.8182 (mmt) REVERT: A 13 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7210 (pp20) REVERT: A 96 LYS cc_start: 0.9216 (mmtt) cc_final: 0.9011 (tttm) REVERT: A 124 MET cc_start: 0.9014 (ttp) cc_final: 0.8630 (ttm) outliers start: 11 outliers final: 7 residues processed: 117 average time/residue: 1.3142 time to fit residues: 173.8046 Evaluate side-chains 115 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 121 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.100523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.069819 restraints weight = 120955.224| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.13 r_work: 0.2972 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17409 Z= 0.135 Angle : 0.504 7.647 23708 Z= 0.268 Chirality : 0.043 0.326 2736 Planarity : 0.004 0.041 2838 Dihedral : 14.258 178.367 2913 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.58 % Allowed : 10.65 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.22 (0.18), residues: 2013 helix: 1.59 (0.21), residues: 643 sheet: 0.83 (0.24), residues: 415 loop : -1.22 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 28 TYR 0.013 0.001 TYR E 227 PHE 0.012 0.001 PHE C 159 TRP 0.006 0.001 TRP G 12 HIS 0.002 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (17408) covalent geometry : angle 0.50424 / 0.27 (23708) hydrogen bonds : bond 0.04512 / 3.03 ( 549) hydrogen bonds : angle 4.16914 / 2.83 ( 1551) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 GLN cc_start: 0.8736 (mp10) cc_final: 0.8479 (mp10) REVERT: F 124 MET cc_start: 0.7938 (ttt) cc_final: 0.7495 (ttt) REVERT: F 248 MET cc_start: 0.5834 (mmm) cc_final: 0.5406 (mmp) REVERT: F 266 ASP cc_start: 0.8592 (m-30) cc_final: 0.8272 (p0) REVERT: F 269 TYR cc_start: 0.7926 (p90) cc_final: 0.7526 (p90) REVERT: F 317 LYS cc_start: 0.9041 (mttt) cc_final: 0.8748 (tptp) REVERT: B 13 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7559 (pp20) REVERT: C 13 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7736 (pp20) REVERT: C 191 ASP cc_start: 0.8445 (p0) cc_final: 0.8213 (p0) REVERT: E 160 HIS cc_start: 0.6818 (m-70) cc_final: 0.6591 (m-70) REVERT: E 193 ASP cc_start: 0.8703 (m-30) cc_final: 0.8336 (m-30) REVERT: E 319 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7807 (mt-10) REVERT: D 13 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7855 (pp20) REVERT: D 260 MET cc_start: 0.8712 (mtm) cc_final: 0.8195 (mmt) REVERT: A 13 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7284 (pp20) REVERT: A 96 LYS cc_start: 0.9213 (mmtt) cc_final: 0.9010 (tttm) REVERT: A 101 TYR cc_start: 0.8507 (m-80) cc_final: 0.8220 (m-80) REVERT: A 124 MET cc_start: 0.8973 (ttp) cc_final: 0.8589 (ttm) outliers start: 9 outliers final: 6 residues processed: 114 average time/residue: 1.3084 time to fit residues: 169.4161 Evaluate side-chains 111 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 108 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 178 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.100883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.070483 restraints weight = 112544.516| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.03 r_work: 0.2987 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17409 Z= 0.108 Angle : 0.484 6.773 23708 Z= 0.256 Chirality : 0.042 0.255 2736 Planarity : 0.004 0.040 2838 Dihedral : 14.228 178.971 2913 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.63 % Allowed : 11.17 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 2013 helix: 1.74 (0.21), residues: 643 sheet: 0.63 (0.23), residues: 435 loop : -1.13 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 174 TYR 0.007 0.001 TYR D 79 PHE 0.011 0.001 PHE C 159 TRP 0.005 0.001 TRP G 12 HIS 0.002 0.000 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (17408) covalent geometry : angle 0.48391 / 0.26 (23708) hydrogen bonds : bond 0.04185 / 2.82 ( 549) hydrogen bonds : angle 4.02533 / 2.74 ( 1551) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 GLN cc_start: 0.8745 (mp10) cc_final: 0.8486 (mp10) REVERT: F 124 MET cc_start: 0.7764 (ttt) cc_final: 0.7546 (ttt) REVERT: F 248 MET cc_start: 0.5834 (mmm) cc_final: 0.5350 (mmp) REVERT: F 266 ASP cc_start: 0.8610 (m-30) cc_final: 0.8267 (p0) REVERT: F 269 TYR cc_start: 0.7953 (p90) cc_final: 0.7574 (p90) REVERT: F 317 LYS cc_start: 0.9043 (mttt) cc_final: 0.8641 (tptp) REVERT: B 13 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7620 (pp20) REVERT: C 13 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7820 (pp20) REVERT: C 191 ASP cc_start: 0.8413 (p0) cc_final: 0.8181 (p0) REVERT: E 160 HIS cc_start: 0.6830 (m-70) cc_final: 0.6556 (m-70) REVERT: E 193 ASP cc_start: 0.8708 (m-30) cc_final: 0.8334 (m-30) REVERT: E 319 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7731 (mt-10) REVERT: D 13 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7891 (pp20) REVERT: D 260 MET cc_start: 0.8696 (mtm) cc_final: 0.8155 (mmt) REVERT: A 13 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7389 (pp20) REVERT: A 101 TYR cc_start: 0.8500 (m-80) cc_final: 0.8213 (m-80) REVERT: A 124 MET cc_start: 0.8960 (ttp) cc_final: 0.8563 (ttm) outliers start: 10 outliers final: 6 residues processed: 109 average time/residue: 1.3340 time to fit residues: 164.3019 Evaluate side-chains 106 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 198 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.099385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.068724 restraints weight = 117552.672| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.07 r_work: 0.2948 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17409 Z= 0.186 Angle : 0.500 6.278 23708 Z= 0.269 Chirality : 0.043 0.269 2736 Planarity : 0.004 0.038 2838 Dihedral : 14.318 179.206 2913 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.86 % Allowed : 11.05 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.09 (0.19), residues: 2013 helix: 1.64 (0.21), residues: 647 sheet: 0.52 (0.24), residues: 424 loop : -1.33 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 28 TYR 0.019 0.001 TYR E 227 PHE 0.015 0.001 PHE C 159 TRP 0.005 0.001 TRP G 12 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (17408) covalent geometry : angle 0.49998 / 0.27 (23708) hydrogen bonds : bond 0.04547 / 3.07 ( 549) hydrogen bonds : angle 4.11334 / 2.80 ( 1551) Misc. bond : bond 0.00066 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 GLN cc_start: 0.8757 (mp10) cc_final: 0.8506 (mp10) REVERT: F 124 MET cc_start: 0.7858 (ttt) cc_final: 0.7619 (ttt) REVERT: F 248 MET cc_start: 0.5884 (mmm) cc_final: 0.5442 (mmp) REVERT: F 266 ASP cc_start: 0.8644 (m-30) cc_final: 0.8295 (p0) REVERT: F 269 TYR cc_start: 0.7976 (p90) cc_final: 0.7579 (p90) REVERT: F 317 LYS cc_start: 0.9031 (mttt) cc_final: 0.8675 (tptp) REVERT: C 13 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8065 (pp20) REVERT: C 112 MET cc_start: 0.9291 (ttp) cc_final: 0.8952 (ttp) REVERT: C 191 ASP cc_start: 0.8519 (p0) cc_final: 0.8264 (p0) REVERT: E 13 GLU cc_start: 0.7060 (pp20) cc_final: 0.6771 (pp20) REVERT: E 154 GLN cc_start: 0.7467 (tp40) cc_final: 0.6951 (tm-30) REVERT: E 193 ASP cc_start: 0.8748 (m-30) cc_final: 0.8361 (m-30) REVERT: E 319 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7745 (mt-10) REVERT: D 13 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8033 (pp20) REVERT: D 260 MET cc_start: 0.8753 (mtm) cc_final: 0.8203 (mmt) REVERT: A 13 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7608 (pp20) REVERT: A 101 TYR cc_start: 0.8508 (m-80) cc_final: 0.8229 (m-80) REVERT: A 124 MET cc_start: 0.8989 (ttp) cc_final: 0.8609 (ttm) outliers start: 14 outliers final: 10 residues processed: 109 average time/residue: 1.2770 time to fit residues: 156.9712 Evaluate side-chains 111 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 120 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 150 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 147 optimal weight: 0.0370 overall best weight: 0.9264 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.100393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.069702 restraints weight = 118563.160| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.10 r_work: 0.2969 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17409 Z= 0.107 Angle : 0.466 6.909 23708 Z= 0.247 Chirality : 0.042 0.268 2736 Planarity : 0.004 0.041 2838 Dihedral : 14.269 179.464 2913 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.63 % Allowed : 11.74 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.22 (0.19), residues: 2013 helix: 1.78 (0.21), residues: 647 sheet: 0.53 (0.24), residues: 425 loop : -1.24 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 174 TYR 0.015 0.001 TYR E 227 PHE 0.013 0.001 PHE C 159 TRP 0.005 0.001 TRP G 12 HIS 0.003 0.001 HIS E 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (17408) covalent geometry : angle 0.46597 / 0.25 (23708) hydrogen bonds : bond 0.03975 / 2.70 ( 549) hydrogen bonds : angle 3.89151 / 2.65 ( 1551) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 GLN cc_start: 0.8764 (mp10) cc_final: 0.8511 (mp10) REVERT: F 248 MET cc_start: 0.5915 (mmm) cc_final: 0.5464 (mmp) REVERT: F 266 ASP cc_start: 0.8640 (m-30) cc_final: 0.8302 (p0) REVERT: F 269 TYR cc_start: 0.8035 (p90) cc_final: 0.7637 (p90) REVERT: F 317 LYS cc_start: 0.9035 (mttt) cc_final: 0.8671 (tptp) REVERT: C 13 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7977 (pp20) REVERT: C 112 MET cc_start: 0.9281 (ttp) cc_final: 0.8961 (ttp) REVERT: C 191 ASP cc_start: 0.8400 (p0) cc_final: 0.8193 (p0) REVERT: E 13 GLU cc_start: 0.7100 (pp20) cc_final: 0.6736 (pp20) REVERT: E 160 HIS cc_start: 0.6779 (m-70) cc_final: 0.6561 (m-70) REVERT: E 193 ASP cc_start: 0.8742 (m-30) cc_final: 0.8351 (m-30) REVERT: E 319 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7750 (mt-10) REVERT: D 13 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8035 (pp20) REVERT: D 101 TYR cc_start: 0.8267 (m-80) cc_final: 0.7887 (m-10) REVERT: D 260 MET cc_start: 0.8717 (mtm) cc_final: 0.8164 (mmt) REVERT: A 13 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7562 (pp20) REVERT: A 101 TYR cc_start: 0.8459 (m-80) cc_final: 0.8170 (m-80) REVERT: A 124 MET cc_start: 0.8968 (ttp) cc_final: 0.8575 (ttm) outliers start: 10 outliers final: 8 residues processed: 104 average time/residue: 1.2431 time to fit residues: 146.7082 Evaluate side-chains 107 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 10 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 147 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 0.0970 chunk 105 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.100453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069876 restraints weight = 116602.463| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.08 r_work: 0.2977 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17409 Z= 0.105 Angle : 0.461 10.138 23708 Z= 0.244 Chirality : 0.042 0.268 2736 Planarity : 0.004 0.040 2838 Dihedral : 14.266 179.711 2913 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.52 % Allowed : 11.80 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.27 (0.19), residues: 2013 helix: 1.79 (0.21), residues: 652 sheet: 0.54 (0.24), residues: 425 loop : -1.20 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 28 TYR 0.020 0.001 TYR E 227 PHE 0.011 0.001 PHE C 159 TRP 0.005 0.001 TRP G 192 HIS 0.002 0.001 HIS F 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (17408) covalent geometry : angle 0.46141 / 0.24 (23708) hydrogen bonds : bond 0.03852 / 2.62 ( 549) hydrogen bonds : angle 3.85157 / 2.62 ( 1551) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 GLN cc_start: 0.8674 (mp10) cc_final: 0.8407 (mp10) REVERT: F 124 MET cc_start: 0.8121 (ttt) cc_final: 0.7880 (ttt) REVERT: F 248 MET cc_start: 0.6044 (mmm) cc_final: 0.5435 (mmm) REVERT: F 266 ASP cc_start: 0.8639 (m-30) cc_final: 0.8317 (p0) REVERT: F 269 TYR cc_start: 0.8108 (p90) cc_final: 0.7715 (p90) REVERT: F 317 LYS cc_start: 0.9087 (mttt) cc_final: 0.8703 (tptp) REVERT: C 13 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7970 (pp20) REVERT: C 112 MET cc_start: 0.9273 (ttp) cc_final: 0.8979 (ttp) REVERT: C 191 ASP cc_start: 0.8387 (p0) cc_final: 0.8179 (p0) REVERT: E 154 GLN cc_start: 0.7565 (tp40) cc_final: 0.7075 (tm-30) REVERT: E 160 HIS cc_start: 0.6774 (m-70) cc_final: 0.6548 (m-70) REVERT: E 193 ASP cc_start: 0.8738 (m-30) cc_final: 0.8345 (m-30) REVERT: E 319 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7749 (mt-10) REVERT: D 13 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8023 (pp20) REVERT: D 101 TYR cc_start: 0.8234 (m-80) cc_final: 0.7849 (m-10) REVERT: D 260 MET cc_start: 0.8720 (mtm) cc_final: 0.8168 (mmt) REVERT: A 13 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7577 (pp20) REVERT: A 101 TYR cc_start: 0.8464 (m-80) cc_final: 0.8172 (m-80) REVERT: A 124 MET cc_start: 0.8959 (ttp) cc_final: 0.8546 (ttm) outliers start: 8 outliers final: 7 residues processed: 105 average time/residue: 1.2838 time to fit residues: 152.4788 Evaluate side-chains 104 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 148 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.099769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.069413 restraints weight = 112543.243| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.99 r_work: 0.2961 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17409 Z= 0.148 Angle : 0.479 9.700 23708 Z= 0.254 Chirality : 0.042 0.266 2736 Planarity : 0.004 0.039 2838 Dihedral : 14.309 179.649 2911 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.75 % Allowed : 11.40 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.21 (0.19), residues: 2013 helix: 1.77 (0.21), residues: 652 sheet: 0.50 (0.24), residues: 425 loop : -1.26 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 28 TYR 0.012 0.001 TYR F 125 PHE 0.013 0.001 PHE C 159 TRP 0.004 0.001 TRP G 12 HIS 0.003 0.001 HIS F 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (17408) covalent geometry : angle 0.47869 / 0.25 (23708) hydrogen bonds : bond 0.04051 / 2.76 ( 549) hydrogen bonds : angle 3.89766 / 2.66 ( 1551) Misc. bond : bond 0.00049 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 GLN cc_start: 0.8602 (mp10) cc_final: 0.8363 (mp10) REVERT: F 124 MET cc_start: 0.8142 (ttt) cc_final: 0.7865 (ttt) REVERT: F 248 MET cc_start: 0.5920 (mmm) cc_final: 0.5332 (mmm) REVERT: F 266 ASP cc_start: 0.8645 (m-30) cc_final: 0.8310 (p0) REVERT: F 269 TYR cc_start: 0.8133 (p90) cc_final: 0.7745 (p90) REVERT: F 317 LYS cc_start: 0.9090 (mttt) cc_final: 0.8705 (tptp) REVERT: C 13 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8024 (pp20) REVERT: C 112 MET cc_start: 0.9271 (ttp) cc_final: 0.8976 (ttp) REVERT: C 191 ASP cc_start: 0.8426 (p0) cc_final: 0.8205 (p0) REVERT: E 154 GLN cc_start: 0.7616 (tp40) cc_final: 0.7111 (tm-30) REVERT: E 193 ASP cc_start: 0.8729 (m-30) cc_final: 0.8318 (m-30) REVERT: E 319 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7737 (mt-10) REVERT: D 13 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8042 (pp20) REVERT: D 260 MET cc_start: 0.8752 (mtm) cc_final: 0.8205 (mmt) REVERT: A 13 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7592 (pp20) REVERT: A 101 TYR cc_start: 0.8457 (m-80) cc_final: 0.8162 (m-80) REVERT: A 124 MET cc_start: 0.8968 (ttp) cc_final: 0.8551 (ttm) outliers start: 12 outliers final: 8 residues processed: 102 average time/residue: 1.1422 time to fit residues: 131.9218 Evaluate side-chains 109 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 133 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.099051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.068619 restraints weight = 113608.340| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.00 r_work: 0.2948 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17409 Z= 0.180 Angle : 0.502 11.415 23708 Z= 0.266 Chirality : 0.042 0.261 2736 Planarity : 0.004 0.039 2838 Dihedral : 14.386 179.261 2911 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.81 % Allowed : 11.46 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.09 (0.19), residues: 2013 helix: 1.67 (0.21), residues: 652 sheet: 0.43 (0.25), residues: 425 loop : -1.33 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 28 TYR 0.032 0.001 TYR E 227 PHE 0.017 0.001 PHE C 159 TRP 0.004 0.001 TRP G 192 HIS 0.003 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (17408) covalent geometry : angle 0.50197 / 0.27 (23708) hydrogen bonds : bond 0.04328 / 2.94 ( 549) hydrogen bonds : angle 3.96728 / 2.70 ( 1551) Misc. bond : bond 0.00073 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 GLN cc_start: 0.8612 (mp10) cc_final: 0.8319 (mp10) REVERT: F 124 MET cc_start: 0.8183 (ttt) cc_final: 0.7848 (ttt) REVERT: F 248 MET cc_start: 0.5853 (mmm) cc_final: 0.5306 (mmm) REVERT: F 266 ASP cc_start: 0.8658 (m-30) cc_final: 0.8329 (p0) REVERT: F 269 TYR cc_start: 0.8148 (p90) cc_final: 0.7747 (p90) REVERT: F 317 LYS cc_start: 0.9082 (mttt) cc_final: 0.8694 (tptp) REVERT: C 13 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8169 (pp20) REVERT: C 112 MET cc_start: 0.9282 (ttp) cc_final: 0.8949 (ttp) REVERT: C 191 ASP cc_start: 0.8468 (p0) cc_final: 0.8191 (p0) REVERT: E 154 GLN cc_start: 0.7696 (tp40) cc_final: 0.7156 (tm-30) REVERT: E 193 ASP cc_start: 0.8743 (m-30) cc_final: 0.8331 (m-30) REVERT: E 319 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7810 (mt-10) REVERT: D 13 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7997 (pp20) REVERT: D 260 MET cc_start: 0.8746 (mtm) cc_final: 0.8208 (mmt) REVERT: A 13 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7686 (pp20) REVERT: A 101 TYR cc_start: 0.8438 (m-80) cc_final: 0.8153 (m-80) REVERT: A 124 MET cc_start: 0.9019 (ttp) cc_final: 0.8599 (ttm) outliers start: 13 outliers final: 9 residues processed: 105 average time/residue: 1.1936 time to fit residues: 142.0297 Evaluate side-chains 107 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 246 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain G residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 97 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.098990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.068477 restraints weight = 116110.078| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.03 r_work: 0.2953 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17409 Z= 0.160 Angle : 0.492 9.990 23708 Z= 0.261 Chirality : 0.042 0.253 2736 Planarity : 0.004 0.039 2838 Dihedral : 14.416 178.929 2911 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.81 % Allowed : 11.51 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.07 (0.19), residues: 2013 helix: 1.66 (0.21), residues: 652 sheet: 0.39 (0.25), residues: 425 loop : -1.33 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 106 TYR 0.009 0.001 TYR E 227 PHE 0.014 0.001 PHE C 159 TRP 0.005 0.001 TRP G 12 HIS 0.003 0.001 HIS F 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (17408) covalent geometry : angle 0.49228 / 0.26 (23708) hydrogen bonds : bond 0.04240 / 2.89 ( 549) hydrogen bonds : angle 3.93462 / 2.68 ( 1551) Misc. bond : bond 0.00070 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8921.53 seconds wall clock time: 151 minutes 53.31 seconds (9113.31 seconds total)