Starting phenix.real_space_refine on Mon Jul 6 13:15:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cp1_45796/07_2026/9cp1_45796_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cp1_45796/07_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_45796/07_2026/9cp1_45796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cp1_45796/07_2026/9cp1_45796.map" model { file = "/net/cci-nas-00/data/ceres_data/9cp1_45796/07_2026/9cp1_45796_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cp1_45796/07_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-dev-6108/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: 6.64, per 1000 atoms: 0.20 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: 3.17 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 6.16 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: 8.31 Time building geometry restraints manager: 4.34 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=" C3' C S 28 " pdb=" C2' C S 28 " pdb=" O2' C S 28 " ideal model delta sigma weight residual 114.60 122.27 -7.67 1.50e+00 4.44e-01 2.61e+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 ... (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: 2135 0.048 - 0.095: 419 0.095 - 0.143: 172 0.143 - 0.190: 4 0.190 - 0.238: 6 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: 1.190 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: 0.240 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 38.400 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.310 ------------------------------------------------------------------------------- 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= 0.186 Angle : 0.525 7.670 23708 Z= 0.328 Chirality : 0.044 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 0.00343 / 0.19 (17408) covalent geometry : angle 0.52537 / 0.33 (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 : 0.896 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: 0.7969 (t) REVERT: F 132 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7527 (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: 0.8728 (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: 0.8706 (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: 1.3810 time to fit residues: 387.9105 Evaluate side-chains 128 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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: 5.9990 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 = 0.3660 r_free = 0.3660 target = 0.100593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.070138 restraints weight = 106709.158| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.97 r_work: 0.2980 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 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 = 0.2988 r_free = 0.2988 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: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17409 Z= 0.177 Angle : 0.562 6.691 23708 Z= 0.301 Chirality : 0.044 0.209 2736 Planarity : 0.005 0.082 2838 Dihedral : 14.400 176.623 2918 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.92 % Allowed : 8.87 % Favored : 90.21 % 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: 0.34 (0.18), residues: 2013 helix: 1.45 (0.21), residues: 643 sheet: 1.02 (0.23), residues: 435 loop : -1.07 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 174 TYR 0.009 0.001 TYR A 141 PHE 0.017 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 0.00401 / 0.18 (17408) covalent geometry : angle 0.56246 / 0.30 (23708) hydrogen bonds : bond 0.05474 / 3.64 ( 549) hydrogen bonds : angle 4.47065 / 3.04 ( 1551) Misc. bond : bond 0.00064 / 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 : 0.812 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: symmetry clash REVERT: F 78 GLN cc_start: 0.8719 (mp10) cc_final: 0.8478 (mp10) REVERT: F 124 MET cc_start: 0.8075 (ttt) cc_final: 0.7685 (ttt) REVERT: F 248 MET cc_start: 0.5835 (mmm) cc_final: 0.5471 (mmp) REVERT: F 266 ASP cc_start: 0.8583 (m-30) cc_final: 0.8297 (p0) REVERT: F 317 LYS cc_start: 0.9018 (mttt) cc_final: 0.8753 (tptp) REVERT: B 13 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7396 (pp20) REVERT: B 151 ILE cc_start: 0.9196 (mt) cc_final: 0.8993 (OUTLIER) REVERT: C 13 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7494 (pp20) REVERT: C 112 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8700 (ttp) REVERT: C 191 ASP cc_start: 0.8394 (p0) cc_final: 0.8189 (p0) REVERT: E 13 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6642 (pp20) REVERT: E 193 ASP cc_start: 0.8605 (m-30) cc_final: 0.8253 (m-30) REVERT: E 319 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7802 (mt-10) REVERT: D 13 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7688 (pp20) REVERT: D 260 MET cc_start: 0.8657 (mtm) cc_final: 0.8179 (mmt) REVERT: A 96 LYS cc_start: 0.9216 (mmtt) cc_final: 0.9012 (tttm) REVERT: A 124 MET cc_start: 0.9029 (ttp) cc_final: 0.8647 (ttm) outliers start: 15 outliers final: 8 residues processed: 138 average time/residue: 1.2803 time to fit residues: 197.5065 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 : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 112 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 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: 9.9990 chunk 68 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 58 GLN B 176 ASN D 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.099103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.068544 restraints weight = 112766.183| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.01 r_work: 0.2948 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- 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 = 0.45 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 = 0.45 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: 0.8255 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17409 Z= 0.232 Angle : 0.551 6.691 23708 Z= 0.298 Chirality : 0.043 0.227 2736 Planarity : 0.004 0.045 2838 Dihedral : 14.410 177.734 2913 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.92 % Allowed : 10.13 % Favored : 88.95 % 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: -0.08 (0.18), residues: 2013 helix: 1.33 (0.21), residues: 643 sheet: 0.60 (0.23), residues: 424 loop : -1.39 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 174 TYR 0.010 0.001 TYR D 79 PHE 0.016 0.001 PHE C 159 TRP 0.007 0.001 TRP G 12 HIS 0.003 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (17408) covalent geometry : angle 0.55118 / 0.30 (23708) hydrogen bonds : bond 0.05366 / 3.59 ( 549) hydrogen bonds : angle 4.42425 / 3.01 ( 1551) Misc. bond : bond 0.00075 / 0.04 ( 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 123 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.769 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: 0.8739 (mp10) cc_final: 0.8487 (mp10) REVERT: F 124 MET cc_start: 0.8096 (ttt) cc_final: 0.7882 (ttt) REVERT: F 248 MET cc_start: 0.5791 (mmm) cc_final: 0.5387 (mmp) REVERT: F 266 ASP cc_start: 0.8587 (m-30) cc_final: 0.8266 (p0) REVERT: F 269 TYR cc_start: 0.7914 (p90) cc_final: 0.7505 (p90) REVERT: F 308 LEU cc_start: 0.4977 (OUTLIER) cc_final: 0.4255 (mp) REVERT: F 317 LYS cc_start: 0.9044 (mttt) cc_final: 0.8742 (tptp) REVERT: C 13 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7591 (pp20) REVERT: C 112 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8819 (ttp) REVERT: C 191 ASP cc_start: 0.8531 (p0) cc_final: 0.8300 (p0) REVERT: E 154 GLN cc_start: 0.7395 (tp40) cc_final: 0.6918 (tm-30) REVERT: E 193 ASP cc_start: 0.8729 (m-30) cc_final: 0.8362 (m-30) REVERT: E 301 VAL cc_start: 0.8938 (p) cc_final: 0.8639 (m) REVERT: E 319 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7786 (mt-10) REVERT: D 13 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7897 (pp20) REVERT: D 260 MET cc_start: 0.8740 (mtm) cc_final: 0.8216 (mmt) REVERT: A 13 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7406 (pp20) REVERT: A 96 LYS cc_start: 0.9214 (mmtt) cc_final: 0.9013 (tttm) REVERT: A 112 MET cc_start: 0.8714 (mtp) cc_final: 0.8511 (mtm) REVERT: A 124 MET cc_start: 0.9036 (ttp) cc_final: 0.8662 (ttm) outliers start: 15 outliers final: 8 residues processed: 115 average time/residue: 1.1608 time to fit residues: 151.2815 Evaluate side-chains 114 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain E residue 96 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 121 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.099900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.069185 restraints weight = 121443.284| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.11 r_work: 0.2962 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17409 Z= 0.140 Angle : 0.514 7.888 23708 Z= 0.274 Chirality : 0.044 0.331 2736 Planarity : 0.004 0.042 2838 Dihedral : 14.391 178.224 2913 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.92 % Allowed : 11.00 % 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: 0.05 (0.18), residues: 2013 helix: 1.49 (0.21), residues: 643 sheet: 0.70 (0.24), residues: 414 loop : -1.34 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 174 TYR 0.012 0.001 TYR E 227 PHE 0.014 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 0.00324 / 0.14 (17408) covalent geometry : angle 0.51449 / 0.27 (23708) hydrogen bonds : bond 0.04653 / 3.12 ( 549) hydrogen bonds : angle 4.19898 / 2.86 ( 1551) Misc. bond : bond 0.00044 / 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 118 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.889 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: 0.8738 (mp10) cc_final: 0.8482 (mp10) REVERT: F 124 MET cc_start: 0.7922 (ttt) cc_final: 0.7678 (ttt) REVERT: F 248 MET cc_start: 0.5826 (mmm) cc_final: 0.5401 (mmp) REVERT: F 266 ASP cc_start: 0.8596 (m-30) cc_final: 0.8261 (p0) REVERT: F 269 TYR cc_start: 0.7939 (p90) cc_final: 0.7559 (p90) REVERT: F 317 LYS cc_start: 0.9038 (mttt) cc_final: 0.8745 (tptp) REVERT: C 13 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7791 (pp20) REVERT: C 112 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8852 (ttp) REVERT: C 191 ASP cc_start: 0.8491 (p0) cc_final: 0.8253 (p0) REVERT: E 13 GLU cc_start: 0.7118 (pp20) cc_final: 0.6856 (pp20) REVERT: E 154 GLN cc_start: 0.7362 (tp40) cc_final: 0.6878 (tm-30) REVERT: E 193 ASP cc_start: 0.8729 (m-30) cc_final: 0.8352 (m-30) REVERT: E 319 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7734 (mt-10) REVERT: D 13 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7976 (pp20) REVERT: D 124 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8853 (ttm) REVERT: D 260 MET cc_start: 0.8727 (mtm) cc_final: 0.8206 (mmt) REVERT: A 13 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7507 (pp20) REVERT: A 96 LYS cc_start: 0.9215 (mmtt) cc_final: 0.9012 (tttm) REVERT: A 101 TYR cc_start: 0.8514 (m-80) cc_final: 0.8219 (m-80) REVERT: A 124 MET cc_start: 0.8980 (ttp) cc_final: 0.8602 (ttm) outliers start: 15 outliers final: 6 residues processed: 111 average time/residue: 1.2101 time to fit residues: 152.7299 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 : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 313 ASP Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain D residue 124 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: 2.9990 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 174 optimal weight: 0.2980 chunk 16 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.099749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.069655 restraints weight = 112778.021| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.95 r_work: 0.2970 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 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: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2432 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= 0.138 Angle : 0.495 6.225 23708 Z= 0.265 Chirality : 0.043 0.260 2736 Planarity : 0.004 0.041 2838 Dihedral : 14.390 178.828 2913 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.75 % Allowed : 11.46 % Favored : 87.80 % 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: 0.05 (0.18), residues: 2013 helix: 1.60 (0.21), residues: 643 sheet: 0.52 (0.24), residues: 424 loop : -1.35 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 133 TYR 0.008 0.001 TYR D 79 PHE 0.013 0.001 PHE C 159 TRP 0.005 0.001 TRP G 12 HIS 0.002 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (17408) covalent geometry : angle 0.49513 / 0.26 (23708) hydrogen bonds : bond 0.04483 / 3.02 ( 549) hydrogen bonds : angle 4.10525 / 2.80 ( 1551) Misc. bond : bond 0.00041 / 0.02 ( 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 112 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.910 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: 0.8748 (mp10) cc_final: 0.8494 (mp10) REVERT: F 124 MET cc_start: 0.7767 (ttt) cc_final: 0.7482 (ttt) REVERT: F 248 MET cc_start: 0.5870 (mmm) cc_final: 0.5411 (mmp) REVERT: F 266 ASP cc_start: 0.8608 (m-30) cc_final: 0.8260 (p0) REVERT: F 269 TYR cc_start: 0.7990 (p90) cc_final: 0.7609 (p90) REVERT: F 317 LYS cc_start: 0.9039 (mttt) cc_final: 0.8644 (tptp) REVERT: C 13 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7960 (pp20) REVERT: C 112 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8882 (ttp) REVERT: C 191 ASP cc_start: 0.8487 (p0) cc_final: 0.8247 (p0) REVERT: E 154 GLN cc_start: 0.7412 (tp40) cc_final: 0.6919 (tm-30) REVERT: E 160 HIS cc_start: 0.6880 (m-70) cc_final: 0.6675 (m-70) REVERT: E 193 ASP cc_start: 0.8711 (m-30) cc_final: 0.8326 (m-30) REVERT: E 319 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7734 (mt-10) REVERT: D 13 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7895 (pp20) REVERT: D 260 MET cc_start: 0.8701 (mtm) cc_final: 0.8162 (mmt) REVERT: A 13 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7540 (pp20) REVERT: A 101 TYR cc_start: 0.8511 (m-80) cc_final: 0.8227 (m-80) REVERT: A 124 MET cc_start: 0.8974 (ttp) cc_final: 0.8587 (ttm) outliers start: 12 outliers final: 6 residues processed: 104 average time/residue: 1.2382 time to fit residues: 146.5205 Evaluate side-chains 105 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain C residue 112 MET 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 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: 0.6980 chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.098909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.068258 restraints weight = 117960.434| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.07 r_work: 0.2939 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 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 = 0.2945 r_free = 0.2945 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: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17409 Z= 0.205 Angle : 0.509 7.274 23708 Z= 0.275 Chirality : 0.043 0.261 2736 Planarity : 0.004 0.040 2838 Dihedral : 14.477 179.193 2913 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.75 % Allowed : 11.92 % Favored : 87.33 % 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: -0.07 (0.18), residues: 2013 helix: 1.51 (0.21), residues: 647 sheet: 0.42 (0.24), residues: 424 loop : -1.43 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 133 TYR 0.018 0.001 TYR E 227 PHE 0.015 0.001 PHE C 159 TRP 0.006 0.001 TRP G 12 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (17408) covalent geometry : angle 0.50851 / 0.27 (23708) hydrogen bonds : bond 0.04703 / 3.18 ( 549) hydrogen bonds : angle 4.17043 / 2.84 ( 1551) Misc. bond : bond 0.00092 / 0.04 ( 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 111 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.021 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: 0.8665 (mp10) cc_final: 0.8400 (mp10) REVERT: F 124 MET cc_start: 0.7840 (ttt) cc_final: 0.7632 (ttt) REVERT: F 248 MET cc_start: 0.5832 (mmm) cc_final: 0.5360 (mmp) REVERT: F 266 ASP cc_start: 0.8644 (m-30) cc_final: 0.8310 (p0) REVERT: F 269 TYR cc_start: 0.8010 (p90) cc_final: 0.7619 (p90) REVERT: F 317 LYS cc_start: 0.9081 (mttt) cc_final: 0.8703 (tptp) REVERT: C 13 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7984 (pp20) REVERT: C 112 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8910 (ttp) REVERT: C 191 ASP cc_start: 0.8537 (p0) cc_final: 0.8254 (p0) REVERT: E 13 GLU cc_start: 0.7177 (pp20) cc_final: 0.6802 (pp20) REVERT: E 154 GLN cc_start: 0.7506 (tp40) cc_final: 0.6987 (tm-30) REVERT: E 193 ASP cc_start: 0.8727 (m-30) cc_final: 0.8318 (m-30) REVERT: E 319 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7758 (mt-10) REVERT: D 13 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8060 (pp20) REVERT: D 260 MET cc_start: 0.8750 (mtm) cc_final: 0.8206 (mmt) REVERT: A 13 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7679 (pp20) REVERT: A 101 TYR cc_start: 0.8528 (m-80) cc_final: 0.8249 (m-80) REVERT: A 124 MET cc_start: 0.8990 (ttp) cc_final: 0.8601 (ttm) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 1.2273 time to fit residues: 145.7319 Evaluate side-chains 108 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 112 MET Chi-restraints excluded: chain C residue 142 MET 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 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: 0.7980 chunk 6 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.099761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.069171 restraints weight = 119230.609| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.07 r_work: 0.2962 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- 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 = 0.44 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 = 0.44 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: 0.8244 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17409 Z= 0.123 Angle : 0.479 10.282 23708 Z= 0.255 Chirality : 0.042 0.265 2736 Planarity : 0.004 0.041 2838 Dihedral : 14.441 179.643 2913 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.98 % Allowed : 11.86 % Favored : 87.16 % 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: 0.06 (0.19), residues: 2013 helix: 1.69 (0.21), residues: 643 sheet: 0.44 (0.24), residues: 425 loop : -1.36 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 28 TYR 0.012 0.001 TYR E 227 PHE 0.013 0.001 PHE C 159 TRP 0.005 0.001 TRP G 192 HIS 0.002 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (17408) covalent geometry : angle 0.47886 / 0.26 (23708) hydrogen bonds : bond 0.04164 / 2.82 ( 549) hydrogen bonds : angle 3.97093 / 2.70 ( 1551) Misc. bond : bond 0.00032 / 0.02 ( 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 113 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.926 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: 0.8666 (mp10) cc_final: 0.8402 (mp10) REVERT: F 124 MET cc_start: 0.7790 (ttt) cc_final: 0.7586 (ttt) REVERT: F 248 MET cc_start: 0.6044 (mmm) cc_final: 0.5469 (mmm) REVERT: F 266 ASP cc_start: 0.8642 (m-30) cc_final: 0.8321 (p0) REVERT: F 269 TYR cc_start: 0.8088 (p90) cc_final: 0.7697 (p90) REVERT: F 317 LYS cc_start: 0.9084 (mttt) cc_final: 0.8705 (tptp) REVERT: C 13 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8042 (pp20) REVERT: C 112 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8926 (ttp) REVERT: C 191 ASP cc_start: 0.8427 (p0) cc_final: 0.8220 (p0) REVERT: E 13 GLU cc_start: 0.7208 (pp20) cc_final: 0.6839 (pp20) REVERT: E 154 GLN cc_start: 0.7593 (tp40) cc_final: 0.7076 (tm-30) REVERT: E 160 HIS cc_start: 0.6379 (m-70) cc_final: 0.6089 (m-70) REVERT: E 193 ASP cc_start: 0.8727 (m-30) cc_final: 0.8313 (m-30) REVERT: E 319 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7666 (mt-10) REVERT: D 13 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7968 (pp20) REVERT: D 260 MET cc_start: 0.8715 (mtm) cc_final: 0.8163 (mmt) REVERT: A 13 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7623 (pp20) REVERT: A 101 TYR cc_start: 0.8515 (m-80) cc_final: 0.8236 (m-80) REVERT: A 124 MET cc_start: 0.8968 (ttp) cc_final: 0.8563 (ttm) outliers start: 16 outliers final: 10 residues processed: 104 average time/residue: 1.1823 time to fit residues: 139.3930 Evaluate side-chains 110 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 112 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 10 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.098484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.068242 restraints weight = 117008.885| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.99 r_work: 0.2934 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17409 Z= 0.207 Angle : 0.509 8.988 23708 Z= 0.274 Chirality : 0.043 0.274 2736 Planarity : 0.004 0.041 2838 Dihedral : 14.528 179.674 2913 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.86 % Allowed : 12.09 % Favored : 87.05 % 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: 1.52 (0.21), residues: 652 sheet: 0.36 (0.24), residues: 425 loop : -1.46 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 28 TYR 0.023 0.001 TYR E 227 PHE 0.016 0.001 PHE C 159 TRP 0.004 0.001 TRP G 192 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (17408) covalent geometry : angle 0.50931 / 0.27 (23708) hydrogen bonds : bond 0.04604 / 3.13 ( 549) hydrogen bonds : angle 4.09824 / 2.79 ( 1551) Misc. bond : bond 0.00087 / 0.04 ( 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: 14 poor density : 95 time to evaluate : 0.933 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: 0.8601 (mp10) cc_final: 0.8357 (mp10) REVERT: F 124 MET cc_start: 0.7807 (ttt) cc_final: 0.7589 (ttt) REVERT: F 248 MET cc_start: 0.5980 (mmm) cc_final: 0.5406 (mmm) REVERT: F 266 ASP cc_start: 0.8640 (m-30) cc_final: 0.8323 (p0) REVERT: F 269 TYR cc_start: 0.8158 (p90) cc_final: 0.7770 (p90) REVERT: F 317 LYS cc_start: 0.9077 (mttt) cc_final: 0.8691 (tptp) REVERT: C 13 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8088 (pp20) REVERT: C 112 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8938 (ttp) REVERT: C 191 ASP cc_start: 0.8502 (p0) cc_final: 0.8222 (p0) REVERT: E 13 GLU cc_start: 0.7314 (pp20) cc_final: 0.6964 (pp20) REVERT: E 154 GLN cc_start: 0.7611 (tp40) cc_final: 0.7084 (tm-30) REVERT: E 193 ASP cc_start: 0.8749 (m-30) cc_final: 0.8324 (m-30) REVERT: E 319 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7748 (mt-10) REVERT: D 13 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8014 (pp20) REVERT: D 101 TYR cc_start: 0.8308 (m-80) cc_final: 0.7915 (m-10) REVERT: D 260 MET cc_start: 0.8765 (mtm) cc_final: 0.8212 (mmt) REVERT: A 13 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7712 (pp20) REVERT: A 101 TYR cc_start: 0.8515 (m-80) cc_final: 0.8232 (m-80) REVERT: A 124 MET cc_start: 0.8991 (ttp) cc_final: 0.8601 (ttm) outliers start: 14 outliers final: 10 residues processed: 103 average time/residue: 1.1870 time to fit residues: 138.7005 Evaluate side-chains 109 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain E residue 100 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 148 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.099809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.069373 restraints weight = 112462.231| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.00 r_work: 0.2964 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 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: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2761 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= 0.104 Angle : 0.475 8.992 23708 Z= 0.252 Chirality : 0.042 0.268 2736 Planarity : 0.004 0.042 2838 Dihedral : 14.481 179.739 2913 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.09 % Allowed : 12.09 % Favored : 86.82 % 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: 0.06 (0.19), residues: 2013 helix: 1.66 (0.21), residues: 652 sheet: 0.40 (0.25), residues: 425 loop : -1.34 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 28 TYR 0.012 0.001 TYR E 227 PHE 0.013 0.001 PHE C 159 TRP 0.006 0.001 TRP G 192 HIS 0.002 0.001 HIS F 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (17408) covalent geometry : angle 0.47476 / 0.25 (23708) hydrogen bonds : bond 0.04018 / 2.74 ( 549) hydrogen bonds : angle 3.88008 / 2.64 ( 1551) Misc. bond : bond 0.00021 / 0.01 ( 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 116 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.870 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: 0.8591 (mp10) cc_final: 0.8358 (mp10) REVERT: F 124 MET cc_start: 0.7461 (ttt) cc_final: 0.7252 (ttt) REVERT: F 248 MET cc_start: 0.5917 (mmm) cc_final: 0.5366 (mmm) REVERT: F 266 ASP cc_start: 0.8656 (m-30) cc_final: 0.8327 (p0) REVERT: F 269 TYR cc_start: 0.8128 (p90) cc_final: 0.7732 (p90) REVERT: F 317 LYS cc_start: 0.9089 (mttt) cc_final: 0.8706 (tptp) REVERT: B 13 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7885 (pp20) REVERT: C 13 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8164 (pp20) REVERT: C 112 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8941 (ttp) REVERT: C 124 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8064 (ttt) REVERT: C 191 ASP cc_start: 0.8456 (p0) cc_final: 0.8166 (p0) REVERT: E 154 GLN cc_start: 0.7569 (tp40) cc_final: 0.7152 (tm-30) REVERT: E 193 ASP cc_start: 0.8729 (m-30) cc_final: 0.8306 (m-30) REVERT: E 319 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7747 (mt-10) REVERT: D 13 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7983 (pp20) REVERT: D 260 MET cc_start: 0.8701 (mtm) cc_final: 0.8157 (mmt) REVERT: A 13 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7615 (pp20) REVERT: A 101 TYR cc_start: 0.8469 (m-80) cc_final: 0.8173 (m-80) REVERT: A 124 MET cc_start: 0.8968 (ttp) cc_final: 0.8570 (ttm) outliers start: 18 outliers final: 9 residues processed: 105 average time/residue: 1.1724 time to fit residues: 138.9512 Evaluate side-chains 111 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 124 MET 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 133 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.098700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.068138 restraints weight = 113956.932| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.02 r_work: 0.2946 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 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 = 0.2942 r_free = 0.2942 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: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 0.036 17409 Z= 0.182 Angle : 0.499 9.020 23708 Z= 0.267 Chirality : 0.042 0.270 2736 Planarity : 0.004 0.040 2838 Dihedral : 14.533 179.715 2911 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.86 % Allowed : 12.09 % Favored : 87.05 % 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: -0.04 (0.19), residues: 2013 helix: 1.60 (0.21), residues: 652 sheet: 0.33 (0.25), residues: 425 loop : -1.42 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 28 TYR 0.028 0.001 TYR E 227 PHE 0.015 0.001 PHE C 159 TRP 0.005 0.001 TRP G 192 HIS 0.003 0.001 HIS F 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (17408) covalent geometry : angle 0.49913 / 0.27 (23708) hydrogen bonds : bond 0.04403 / 2.99 ( 549) hydrogen bonds : angle 4.00858 / 2.73 ( 1551) Misc. bond : bond 0.00065 / 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 110 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.876 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: 0.8594 (mp10) cc_final: 0.8308 (mp10) REVERT: F 248 MET cc_start: 0.5960 (mmm) cc_final: 0.5407 (mmm) REVERT: F 266 ASP cc_start: 0.8665 (m-30) cc_final: 0.8327 (p0) REVERT: F 269 TYR cc_start: 0.8169 (p90) cc_final: 0.7776 (p90) REVERT: F 317 LYS cc_start: 0.9080 (mttt) cc_final: 0.8692 (tptp) REVERT: B 13 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8023 (pp20) REVERT: C 13 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8112 (pp20) REVERT: C 112 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8966 (ttp) REVERT: C 191 ASP cc_start: 0.8516 (p0) cc_final: 0.8197 (p0) REVERT: E 13 GLU cc_start: 0.6899 (pp20) cc_final: 0.6676 (pp20) REVERT: E 154 GLN cc_start: 0.7640 (tp40) cc_final: 0.7186 (tm-30) REVERT: E 193 ASP cc_start: 0.8756 (m-30) cc_final: 0.8328 (m-30) REVERT: E 319 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7734 (mt-10) REVERT: D 13 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8021 (pp20) REVERT: D 260 MET cc_start: 0.8750 (mtm) cc_final: 0.8207 (mmt) REVERT: A 13 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7736 (pp20) REVERT: A 101 TYR cc_start: 0.8490 (m-80) cc_final: 0.8203 (m-80) REVERT: A 124 MET cc_start: 0.9023 (ttp) cc_final: 0.8608 (ttm) outliers start: 14 outliers final: 9 residues processed: 102 average time/residue: 1.2088 time to fit residues: 138.8858 Evaluate side-chains 109 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 124 MET 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: 0.5980 chunk 202 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.098855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.068597 restraints weight = 115724.288| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.98 r_work: 0.2945 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17409 Z= 0.154 Angle : 0.490 8.686 23708 Z= 0.261 Chirality : 0.042 0.263 2736 Planarity : 0.004 0.045 2838 Dihedral : 14.532 179.558 2911 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.98 % Allowed : 11.92 % Favored : 87.10 % 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: -0.02 (0.19), residues: 2013 helix: 1.61 (0.21), residues: 652 sheet: 0.32 (0.25), residues: 425 loop : -1.39 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 106 TYR 0.012 0.001 TYR E 227 PHE 0.015 0.001 PHE C 159 TRP 0.006 0.001 TRP G 192 HIS 0.003 0.001 HIS F 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (17408) covalent geometry : angle 0.49019 / 0.26 (23708) hydrogen bonds : bond 0.04268 / 2.91 ( 549) hydrogen bonds : angle 3.94799 / 2.69 ( 1551) Misc. bond : bond 0.00065 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8861.36 seconds wall clock time: 150 minutes 46.54 seconds (9046.54 seconds total)