Starting phenix.real_space_refine on Mon Oct 26 20:47:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ojj_70536/10_2026/9ojj_70536.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ojj_70536/10_2026/9ojj_70536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ojj_70536/10_2026/9ojj_70536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ojj_70536/10_2026/9ojj_70536.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ojj_70536/10_2026/9ojj_70536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ojj_70536/10_2026/9ojj_70536.map" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 92 5.16 5 C 6872 2.51 5 N 1826 2.21 5 O 2149 1.98 5 H 10695 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21634 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 952 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "B" Number of atoms: 938 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 58, 937 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Conformer: "B" Number of residues, atoms: 58, 937 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} bond proxies already assigned to first conformer: 941 Chain: "C" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 940 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "D" Number of atoms: 926 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 57, 925 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Conformer: "B" Number of residues, atoms: 57, 925 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} bond proxies already assigned to first conformer: 929 Chain: "E" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4467 Classifications: {'peptide': 287} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain: "F" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4468 Classifications: {'peptide': 287} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain: "G" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4467 Classifications: {'peptide': 287} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain: "I" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4467 Classifications: {'peptide': 287} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 3.67, per 1000 atoms: 0.17 Number of scatterers: 21634 At special positions: 0 Unit cell: (119.464, 116.176, 97.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 O 2149 8.00 N 1826 7.00 C 6872 6.00 H 10695 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=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 645.9 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 95.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 194 through 252 removed outlier: 3.571A pdb=" N MET A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 252 removed outlier: 3.660A pdb=" N ASP B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA B 220 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET B 221 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 222 " --> pdb=" O ASP B 218 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 253 removed outlier: 3.918A pdb=" N LYS C 204 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 217 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 222 " --> pdb=" O ASP C 218 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 253 removed outlier: 3.664A pdb=" N LEU D 222 " --> pdb=" O ASP D 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 31 removed outlier: 3.852A pdb=" N GLN E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 55 Processing helix chain 'E' and resid 57 through 74 removed outlier: 3.681A pdb=" N GLN E 74 " --> pdb=" O GLN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 96 removed outlier: 4.139A pdb=" N LYS E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 113 removed outlier: 3.977A pdb=" N ALA E 100 " --> pdb=" O ASP E 96 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 134 removed outlier: 3.876A pdb=" N ALA E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 154 Processing helix chain 'E' and resid 157 through 175 removed outlier: 3.950A pdb=" N GLN E 174 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU E 175 " --> pdb=" O TYR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 194 removed outlier: 4.053A pdb=" N ASP E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 200 removed outlier: 3.777A pdb=" N LEU E 198 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR E 200 " --> pdb=" O LEU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 217 removed outlier: 3.935A pdb=" N TYR E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE E 207 " --> pdb=" O LYS E 203 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE E 216 " --> pdb=" O CYS E 212 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP E 217 " --> pdb=" O HIS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 220 No H-bonds generated for 'chain 'E' and resid 218 through 220' Processing helix chain 'E' and resid 221 through 232 removed outlier: 3.530A pdb=" N LEU E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 removed outlier: 4.184A pdb=" N ASP E 237 " --> pdb=" O PRO E 233 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 233 through 238' Processing helix chain 'E' and resid 238 through 252 removed outlier: 3.888A pdb=" N LYS E 242 " --> pdb=" O SER E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 270 removed outlier: 3.858A pdb=" N TYR E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL E 263 " --> pdb=" O TYR E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 286 Processing helix chain 'F' and resid 1 through 32 removed outlier: 3.909A pdb=" N GLN F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 56 Processing helix chain 'F' and resid 57 through 75 removed outlier: 3.597A pdb=" N ALA F 61 " --> pdb=" O ASN F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 96 removed outlier: 4.608A pdb=" N LYS F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 115 removed outlier: 3.967A pdb=" N ALA F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE F 101 " --> pdb=" O PRO F 97 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 134 removed outlier: 3.657A pdb=" N ALA F 120 " --> pdb=" O ARG F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 154 removed outlier: 3.544A pdb=" N ALA F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 173 removed outlier: 3.636A pdb=" N ALA F 161 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS F 164 " --> pdb=" O SER F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.793A pdb=" N ILE F 184 " --> pdb=" O LYS F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 195 No H-bonds generated for 'chain 'F' and resid 194 through 195' Processing helix chain 'F' and resid 196 through 200 removed outlier: 3.664A pdb=" N TYR F 200 " --> pdb=" O LEU F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 217 removed outlier: 4.213A pdb=" N TYR F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE F 216 " --> pdb=" O CYS F 212 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP F 217 " --> pdb=" O HIS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 232 removed outlier: 3.795A pdb=" N ALA F 221 " --> pdb=" O ASP F 217 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS F 222 " --> pdb=" O MET F 218 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU F 231 " --> pdb=" O LYS F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 removed outlier: 4.148A pdb=" N ASP F 237 " --> pdb=" O PRO F 233 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER F 238 " --> pdb=" O ALA F 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 233 through 238' Processing helix chain 'F' and resid 238 through 252 removed outlier: 4.103A pdb=" N LYS F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 270 Processing helix chain 'F' and resid 273 through 286 removed outlier: 4.075A pdb=" N THR F 286 " --> pdb=" O ARG F 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 32 removed outlier: 4.028A pdb=" N GLN G 25 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 55 removed outlier: 4.267A pdb=" N ILE G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 75 removed outlier: 3.742A pdb=" N ALA G 61 " --> pdb=" O ASN G 57 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 96 removed outlier: 4.433A pdb=" N LYS G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA G 95 " --> pdb=" O ALA G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 115 removed outlier: 4.488A pdb=" N ALA G 100 " --> pdb=" O ASP G 96 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE G 101 " --> pdb=" O PRO G 97 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS G 103 " --> pdb=" O GLU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 134 removed outlier: 3.936A pdb=" N ALA G 120 " --> pdb=" O ARG G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 154 removed outlier: 3.602A pdb=" N ALA G 141 " --> pdb=" O ASP G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 173 Processing helix chain 'G' and resid 174 through 176 No H-bonds generated for 'chain 'G' and resid 174 through 176' Processing helix chain 'G' and resid 178 through 194 removed outlier: 3.531A pdb=" N ILE G 184 " --> pdb=" O LYS G 180 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP G 194 " --> pdb=" O THR G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 200 removed outlier: 3.672A pdb=" N LEU G 198 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR G 200 " --> pdb=" O LEU G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 215 removed outlier: 4.036A pdb=" N TYR G 205 " --> pdb=" O SER G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 220 Processing helix chain 'G' and resid 221 through 232 Processing helix chain 'G' and resid 233 through 238 removed outlier: 4.190A pdb=" N ASP G 237 " --> pdb=" O PRO G 233 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER G 238 " --> pdb=" O ALA G 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 233 through 238' Processing helix chain 'G' and resid 238 through 253 removed outlier: 4.226A pdb=" N LYS G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU G 243 " --> pdb=" O ARG G 239 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 270 removed outlier: 3.800A pdb=" N TYR G 259 " --> pdb=" O ASN G 255 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU G 261 " --> pdb=" O ASP G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 285 Processing helix chain 'I' and resid 1 through 31 removed outlier: 4.026A pdb=" N GLN I 25 " --> pdb=" O VAL I 21 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 55 removed outlier: 4.195A pdb=" N ALA I 55 " --> pdb=" O MET I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 75 removed outlier: 3.613A pdb=" N LEU I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 93 Processing helix chain 'I' and resid 96 through 114 removed outlier: 4.302A pdb=" N ALA I 100 " --> pdb=" O ASP I 96 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN I 102 " --> pdb=" O GLN I 98 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS I 103 " --> pdb=" O GLU I 99 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET I 114 " --> pdb=" O ILE I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 134 removed outlier: 3.616A pdb=" N ALA I 120 " --> pdb=" O ARG I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 154 Processing helix chain 'I' and resid 157 through 175 Processing helix chain 'I' and resid 178 through 194 removed outlier: 4.100A pdb=" N ASP I 194 " --> pdb=" O THR I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 200 removed outlier: 3.823A pdb=" N LEU I 198 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR I 200 " --> pdb=" O LEU I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 217 removed outlier: 4.026A pdb=" N TYR I 205 " --> pdb=" O SER I 201 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE I 216 " --> pdb=" O CYS I 212 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP I 217 " --> pdb=" O HIS I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 232 removed outlier: 4.255A pdb=" N LYS I 222 " --> pdb=" O MET I 218 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU I 223 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU I 230 " --> pdb=" O GLN I 226 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU I 231 " --> pdb=" O LYS I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 237 Processing helix chain 'I' and resid 238 through 253 removed outlier: 3.645A pdb=" N LYS I 242 " --> pdb=" O SER I 238 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU I 253 " --> pdb=" O GLU I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 270 Processing helix chain 'I' and resid 273 through 286 removed outlier: 3.794A pdb=" N THR I 286 " --> pdb=" O ARG I 282 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2757 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.88 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10663 1.03 - 1.22: 40 1.22 - 1.42: 4691 1.42 - 1.61: 6259 1.61 - 1.81: 152 Bond restraints: 21805 Sorted by residual: bond pdb=" C GLU F 186 " pdb=" O GLU F 186 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.16e-02 7.43e+03 1.77e+01 bond pdb=" N VAL G 168 " pdb=" CA VAL G 168 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.30e-02 5.92e+03 8.50e+00 bond pdb=" C VAL G 168 " pdb=" O VAL G 168 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.29e-02 6.01e+03 7.47e+00 bond pdb=" N ASP I 80 " pdb=" H ASP I 80 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" N TYR F 171 " pdb=" H TYR F 171 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.88e+00 ... (remaining 21800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 39078 1.99 - 3.99: 206 3.99 - 5.98: 14 5.98 - 7.97: 1 7.97 - 9.96: 3 Bond angle restraints: 39302 Sorted by residual: angle pdb=" N TYR F 171 " pdb=" CA TYR F 171 " pdb=" C TYR F 171 " ideal model delta sigma weight residual 111.69 105.96 5.73 1.23e+00 6.61e-01 2.17e+01 angle pdb=" N GLU F 186 " pdb=" CA GLU F 186 " pdb=" C GLU F 186 " ideal model delta sigma weight residual 111.02 105.81 5.21 1.22e+00 6.72e-01 1.83e+01 angle pdb=" N ASP I 80 " pdb=" CA ASP I 80 " pdb=" C ASP I 80 " ideal model delta sigma weight residual 111.36 107.00 4.36 1.09e+00 8.42e-01 1.60e+01 angle pdb=" N TYR E 228 " pdb=" CA TYR E 228 " pdb=" C TYR E 228 " ideal model delta sigma weight residual 111.14 106.98 4.16 1.08e+00 8.57e-01 1.48e+01 angle pdb=" N LYS F 140 " pdb=" CA LYS F 140 " pdb=" C LYS F 140 " ideal model delta sigma weight residual 111.07 107.04 4.03 1.07e+00 8.73e-01 1.42e+01 ... (remaining 39297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 9458 17.90 - 35.79: 589 35.79 - 53.69: 155 53.69 - 71.58: 38 71.58 - 89.48: 9 Dihedral angle restraints: 10249 sinusoidal: 5444 harmonic: 4805 Sorted by residual: dihedral pdb=" CA GLN F 177 " pdb=" C GLN F 177 " pdb=" N TYR F 178 " pdb=" CA TYR F 178 " ideal model delta harmonic sigma weight residual -180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA GLN G 177 " pdb=" C GLN G 177 " pdb=" N TYR G 178 " pdb=" CA TYR G 178 " ideal model delta harmonic sigma weight residual -180.00 -160.96 -19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA SER G 157 " pdb=" C SER G 157 " pdb=" N ASN G 158 " pdb=" CA ASN G 158 " ideal model delta harmonic sigma weight residual -180.00 -161.29 -18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 10246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1327 0.037 - 0.075: 258 0.075 - 0.112: 34 0.112 - 0.150: 4 0.150 - 0.187: 3 Chirality restraints: 1626 Sorted by residual: chirality pdb=" CA HIS I 72 " pdb=" N HIS I 72 " pdb=" C HIS I 72 " pdb=" CB HIS I 72 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA LYS F 140 " pdb=" N LYS F 140 " pdb=" C LYS F 140 " pdb=" CB LYS F 140 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA GLU F 186 " pdb=" N GLU F 186 " pdb=" C GLU F 186 " pdb=" CB GLU F 186 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 1623 not shown) Planarity restraints: 3286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 220 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.43e+00 pdb=" C ASN F 220 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN F 220 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA F 221 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 186 " 0.013 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" N GLN F 187 " -0.042 2.00e-02 2.50e+03 pdb=" CA GLN F 187 " 0.011 2.00e-02 2.50e+03 pdb=" H GLN F 187 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 206 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C PHE E 206 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE E 206 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE E 207 " 0.014 2.00e-02 2.50e+03 ... (remaining 3283 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1374 2.21 - 2.81: 45090 2.81 - 3.40: 58257 3.40 - 4.00: 67469 4.00 - 4.60: 108928 Nonbonded interactions: 281118 Sorted by model distance: nonbonded pdb=" O ILE B 195 " pdb=" H HIS B 199 " model vdw 1.611 2.450 nonbonded pdb=" O GLY E 154 " pdb=" HZ3 LYS F 53 " model vdw 1.653 2.450 nonbonded pdb=" O PRO E 196 " pdb=" HZ2 LYS E 199 " model vdw 1.654 2.450 nonbonded pdb=" OD1 ASN F 63 " pdb="HE22 GLN F 67 " model vdw 1.669 2.450 nonbonded pdb=" OE1 GLN E 98 " pdb=" H GLN E 98 " model vdw 1.677 2.450 ... (remaining 281113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 197 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 198 through 235 or resid 237 through 252)) selection = (chain 'B' and ((resid 197 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 198 through 235 or resid 237 through 252)) selection = (chain 'C' and ((resid 197 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 198 through 235 or resid 237 through 252)) selection = (chain 'D' and (resid 197 through 235 or resid 237 through 252)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 0 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 214 through 286)) selection = chain 'G' selection = chain 'I' } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.300 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 17.810 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.004 0.049 11110 Z= 0.225 Angle : 0.553 5.771 14920 Z= 0.363 Chirality : 0.031 0.187 1626 Planarity : 0.004 0.025 1924 Dihedral : 13.283 89.479 4140 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.35 % Favored : 97.58 % Rotamer: Outliers : 0.95 % Allowed : 7.01 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.75 (0.22), residues: 1364 helix: 2.25 (0.14), residues: 1175 sheet: None (None), residues: 0 loop : -1.01 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 271 TYR 0.024 0.002 TYR D 243 PHE 0.011 0.002 PHE G 235 TRP 0.008 0.002 TRP F 275 HIS 0.007 0.001 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.22 (11110) covalent geometry : angle 0.55327 / 0.36 (14920) hydrogen bonds : bond 0.11424 / 7.85 ( 926) hydrogen bonds : angle 5.28024 / 4.03 ( 2757) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.636 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: A 201 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7329 (mp0) REVERT: D 229 MET cc_start: 0.8351 (mtm) cc_final: 0.8108 (mtm) REVERT: E 11 MET cc_start: 0.9290 (tpp) cc_final: 0.9039 (tpp) REVERT: E 105 MET cc_start: 0.8939 (tpp) cc_final: 0.8668 (mmt) REVERT: G 51 MET cc_start: 0.8565 (ttm) cc_final: 0.8183 (ttm) REVERT: G 279 MET cc_start: 0.9539 (mmm) cc_final: 0.8927 (mpp) REVERT: I 66 CYS cc_start: 0.9593 (t) cc_final: 0.9218 (p) outliers start: 11 outliers final: 5 residues processed: 149 average time/residue: 0.2197 time to fit residues: 46.5694 Evaluate side-chains 107 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 ASN B 239 HIS C 226 GLN F 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.070704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.055395 restraints weight = 146307.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.057878 restraints weight = 67486.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.059470 restraints weight = 40817.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.060397 restraints weight = 29416.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.061003 restraints weight = 24151.304| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11110 Z= 0.153 Angle : 0.470 5.236 14920 Z= 0.283 Chirality : 0.029 0.122 1626 Planarity : 0.003 0.033 1924 Dihedral : 3.890 19.750 1480 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.17 % Allowed : 2.51 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.28 (0.22), residues: 1364 helix: 2.57 (0.14), residues: 1195 sheet: None (None), residues: 0 loop : -0.93 (0.52), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 246 TYR 0.028 0.002 TYR F 131 PHE 0.014 0.001 PHE E 214 TRP 0.007 0.001 TRP I 275 HIS 0.009 0.001 HIS G 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (11110) covalent geometry : angle 0.47023 / 0.28 (14920) hydrogen bonds : bond 0.05803 / 4.01 ( 926) hydrogen bonds : angle 4.24918 / 3.23 ( 2757) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.663 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: symmetry clash REVERT: D 214 ASP cc_start: 0.7980 (t70) cc_final: 0.7497 (t0) REVERT: E 11 MET cc_start: 0.9231 (tpp) cc_final: 0.8920 (tpp) REVERT: E 157 SER cc_start: 0.8853 (m) cc_final: 0.8173 (p) REVERT: F 105 MET cc_start: 0.8765 (mmm) cc_final: 0.8558 (mmt) REVERT: G 51 MET cc_start: 0.8655 (ttm) cc_final: 0.8250 (ttm) REVERT: G 279 MET cc_start: 0.9497 (mmm) cc_final: 0.8857 (mpp) outliers start: 2 outliers final: 1 residues processed: 135 average time/residue: 0.2359 time to fit residues: 45.1815 Evaluate side-chains 105 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [86, 13, 111, 48, 130, 51, 1, 7, 62, 12, 108] chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 23 ASN G 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.069039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.053933 restraints weight = 145126.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.056306 restraints weight = 67148.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.057817 restraints weight = 40777.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.058749 restraints weight = 29581.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.059319 restraints weight = 24202.230| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11110 Z= 0.188 Angle : 0.488 5.033 14920 Z= 0.299 Chirality : 0.029 0.114 1626 Planarity : 0.003 0.032 1924 Dihedral : 3.988 21.289 1480 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.11 (0.22), residues: 1364 helix: 2.43 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.99 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 246 TYR 0.021 0.002 TYR I 131 PHE 0.018 0.002 PHE E 214 TRP 0.007 0.001 TRP F 275 HIS 0.008 0.001 HIS F 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (11110) covalent geometry : angle 0.48784 / 0.30 (14920) hydrogen bonds : bond 0.05814 / 4.03 ( 926) hydrogen bonds : angle 4.35666 / 3.30 ( 2757) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.604 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 ASP cc_start: 0.7909 (t70) cc_final: 0.7446 (t0) REVERT: D 217 MET cc_start: 0.8844 (mmp) cc_final: 0.8584 (mmp) REVERT: E 11 MET cc_start: 0.9220 (tpp) cc_final: 0.8922 (tpp) REVERT: E 105 MET cc_start: 0.8959 (tpp) cc_final: 0.8674 (mmt) REVERT: E 157 SER cc_start: 0.9027 (m) cc_final: 0.8396 (p) REVERT: G 51 MET cc_start: 0.8708 (ttm) cc_final: 0.8361 (ttm) REVERT: G 279 MET cc_start: 0.9499 (mmm) cc_final: 0.8814 (mpp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2135 time to fit residues: 35.5419 Evaluate side-chains 101 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [78, 116, 73, 60, 39, 43, 121, 69, 50, 67, 94] chunk 78 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.070860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055691 restraints weight = 143075.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.058159 restraints weight = 64615.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.059730 restraints weight = 38698.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.060655 restraints weight = 27753.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.061272 restraints weight = 22668.004| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11110 Z= 0.119 Angle : 0.420 5.116 14920 Z= 0.250 Chirality : 0.028 0.109 1626 Planarity : 0.002 0.023 1924 Dihedral : 3.793 20.379 1480 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.63 (0.22), residues: 1364 helix: 2.80 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.99 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.021 0.001 TYR C 235 PHE 0.014 0.001 PHE E 214 TRP 0.007 0.001 TRP I 275 HIS 0.006 0.001 HIS F 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (11110) covalent geometry : angle 0.41977 / 0.25 (14920) hydrogen bonds : bond 0.05018 / 3.49 ( 926) hydrogen bonds : angle 3.84516 / 2.92 ( 2757) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.619 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 ASP cc_start: 0.7970 (t70) cc_final: 0.7462 (t0) REVERT: D 217 MET cc_start: 0.8875 (mmp) cc_final: 0.8581 (mmp) REVERT: E 11 MET cc_start: 0.9221 (tpp) cc_final: 0.8915 (tpp) REVERT: E 157 SER cc_start: 0.8881 (m) cc_final: 0.8300 (p) REVERT: F 255 ASN cc_start: 0.8576 (t0) cc_final: 0.7963 (m110) REVERT: G 51 MET cc_start: 0.8668 (ttm) cc_final: 0.8301 (ttm) REVERT: G 279 MET cc_start: 0.9485 (mmm) cc_final: 0.8817 (mpp) REVERT: I 40 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8402 (mt-10) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2441 time to fit residues: 45.3936 Evaluate side-chains 106 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [63, 35, 24, 83, 108, 111, 126, 82, 21, 38, 30] chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 126 optimal weight: 0.0980 chunk 82 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.067716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.052618 restraints weight = 144373.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.054985 restraints weight = 66555.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.056484 restraints weight = 40439.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057391 restraints weight = 29354.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.057924 restraints weight = 24086.573| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11110 Z= 0.241 Angle : 0.550 8.090 14920 Z= 0.337 Chirality : 0.031 0.218 1626 Planarity : 0.003 0.034 1924 Dihedral : 4.185 23.165 1480 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.62 (0.22), residues: 1364 helix: 2.11 (0.14), residues: 1203 sheet: None (None), residues: 0 loop : -1.12 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 232 TYR 0.021 0.002 TYR B 243 PHE 0.022 0.002 PHE E 214 TRP 0.007 0.001 TRP F 275 HIS 0.008 0.001 HIS F 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.24 (11110) covalent geometry : angle 0.54970 / 0.34 (14920) hydrogen bonds : bond 0.06197 / 4.29 ( 926) hydrogen bonds : angle 4.62526 / 3.51 ( 2757) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.566 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7487 (tm-30) REVERT: D 214 ASP cc_start: 0.8004 (t70) cc_final: 0.7569 (t0) REVERT: E 11 MET cc_start: 0.9220 (tpp) cc_final: 0.8926 (tpp) REVERT: E 105 MET cc_start: 0.8947 (tpp) cc_final: 0.8627 (mmt) REVERT: E 157 SER cc_start: 0.9090 (m) cc_final: 0.8429 (p) REVERT: F 54 MET cc_start: 0.8951 (tmm) cc_final: 0.8696 (tmm) REVERT: F 255 ASN cc_start: 0.8635 (t0) cc_final: 0.7981 (m110) REVERT: G 1 MET cc_start: 0.7871 (tmm) cc_final: 0.7300 (tpt) REVERT: G 51 MET cc_start: 0.8791 (ttm) cc_final: 0.8442 (ttm) REVERT: I 40 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8387 (mt-10) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2203 time to fit residues: 36.6936 Evaluate side-chains 106 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [105, 0, 28, 7, 99, 117, 87, 110, 50, 121, 60] chunk 105 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 50 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.068546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.053289 restraints weight = 145652.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.055683 restraints weight = 66254.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.057207 restraints weight = 40079.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.058122 restraints weight = 28962.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058719 restraints weight = 23729.006| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11110 Z= 0.167 Angle : 0.475 8.360 14920 Z= 0.287 Chirality : 0.030 0.160 1626 Planarity : 0.002 0.020 1924 Dihedral : 4.038 22.536 1480 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.96 (0.22), residues: 1364 helix: 2.34 (0.14), residues: 1203 sheet: None (None), residues: 0 loop : -1.11 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 210 TYR 0.030 0.002 TYR G 259 PHE 0.015 0.002 PHE E 214 TRP 0.008 0.001 TRP E 58 HIS 0.010 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (11110) covalent geometry : angle 0.47520 / 0.29 (14920) hydrogen bonds : bond 0.05527 / 3.84 ( 926) hydrogen bonds : angle 4.23426 / 3.22 ( 2757) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.445 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 ASP cc_start: 0.7895 (t70) cc_final: 0.7534 (t0) REVERT: E 11 MET cc_start: 0.9204 (tpp) cc_final: 0.8907 (tpp) REVERT: E 105 MET cc_start: 0.8928 (tpp) cc_final: 0.8629 (mmt) REVERT: E 157 SER cc_start: 0.9067 (m) cc_final: 0.8457 (p) REVERT: F 23 ASN cc_start: 0.8155 (m110) cc_final: 0.7831 (m110) REVERT: F 54 MET cc_start: 0.9019 (tmm) cc_final: 0.8622 (tmm) REVERT: F 255 ASN cc_start: 0.8669 (t0) cc_final: 0.8091 (m110) REVERT: G 1 MET cc_start: 0.7789 (tmm) cc_final: 0.7290 (tpt) REVERT: G 51 MET cc_start: 0.8718 (ttm) cc_final: 0.8379 (ttm) REVERT: I 40 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8382 (mt-10) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2197 time to fit residues: 38.4726 Evaluate side-chains 103 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [75, 6, 128, 43, 8, 98, 106, 29, 41, 61, 117] chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 29 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.070466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.055246 restraints weight = 143082.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.057734 restraints weight = 65234.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.059284 restraints weight = 39296.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.060221 restraints weight = 28296.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060814 restraints weight = 23145.628| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11110 Z= 0.119 Angle : 0.433 5.935 14920 Z= 0.254 Chirality : 0.028 0.106 1626 Planarity : 0.002 0.019 1924 Dihedral : 3.791 21.447 1480 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.56 (0.22), residues: 1364 helix: 2.76 (0.14), residues: 1195 sheet: None (None), residues: 0 loop : -0.95 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.024 0.001 TYR C 235 PHE 0.014 0.001 PHE F 232 TRP 0.009 0.001 TRP I 275 HIS 0.006 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (11110) covalent geometry : angle 0.43266 / 0.25 (14920) hydrogen bonds : bond 0.04826 / 3.35 ( 926) hydrogen bonds : angle 3.83721 / 2.90 ( 2757) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.424 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: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9192 (mtp) cc_final: 0.8876 (mtp) REVERT: A 245 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7231 (mm-30) REVERT: D 214 ASP cc_start: 0.7918 (t70) cc_final: 0.7320 (t0) REVERT: D 217 MET cc_start: 0.8913 (mmp) cc_final: 0.8653 (mmp) REVERT: D 218 ASP cc_start: 0.8633 (m-30) cc_final: 0.8048 (m-30) REVERT: E 11 MET cc_start: 0.9187 (tpp) cc_final: 0.8958 (tpp) REVERT: E 157 SER cc_start: 0.8885 (m) cc_final: 0.8330 (p) REVERT: F 23 ASN cc_start: 0.8046 (m110) cc_final: 0.7808 (m110) REVERT: F 54 MET cc_start: 0.9047 (tmm) cc_final: 0.8694 (tmm) REVERT: F 255 ASN cc_start: 0.8624 (t0) cc_final: 0.8098 (m110) REVERT: F 279 MET cc_start: 0.9518 (mmm) cc_final: 0.9043 (tpp) REVERT: G 1 MET cc_start: 0.7738 (tmm) cc_final: 0.7326 (tpt) REVERT: G 23 ASN cc_start: 0.8115 (m110) cc_final: 0.7850 (p0) REVERT: G 51 MET cc_start: 0.8680 (ttm) cc_final: 0.8327 (ttm) REVERT: I 40 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8408 (mt-10) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2209 time to fit residues: 38.8473 Evaluate side-chains 108 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [125, 108, 35, 10, 49, 42, 79, 107, 123, 101, 89] chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 255 ASN I 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.070393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.055147 restraints weight = 144557.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.057585 restraints weight = 65913.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.059150 restraints weight = 39705.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.060095 restraints weight = 28631.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060689 restraints weight = 23344.016| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 11110 Z= 0.118 Angle : 0.424 5.443 14920 Z= 0.250 Chirality : 0.028 0.116 1626 Planarity : 0.002 0.019 1924 Dihedral : 3.693 20.932 1480 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.09 % Allowed : 0.52 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.74 (0.22), residues: 1364 helix: 2.89 (0.14), residues: 1195 sheet: None (None), residues: 0 loop : -0.96 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.017 0.001 TYR E 111 PHE 0.014 0.001 PHE F 52 TRP 0.007 0.001 TRP I 275 HIS 0.012 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (11110) covalent geometry : angle 0.42398 / 0.25 (14920) hydrogen bonds : bond 0.04710 / 3.27 ( 926) hydrogen bonds : angle 3.71689 / 2.82 ( 2757) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.597 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: A 219 MET cc_start: 0.9193 (mtp) cc_final: 0.8830 (mtp) REVERT: A 245 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7285 (mm-30) REVERT: D 214 ASP cc_start: 0.7956 (t70) cc_final: 0.7321 (t0) REVERT: D 217 MET cc_start: 0.8904 (mmp) cc_final: 0.8630 (mmp) REVERT: D 218 ASP cc_start: 0.8605 (m-30) cc_final: 0.8003 (m-30) REVERT: E 11 MET cc_start: 0.9194 (tpp) cc_final: 0.8936 (tpp) REVERT: F 23 ASN cc_start: 0.8079 (m110) cc_final: 0.7825 (m110) REVERT: F 54 MET cc_start: 0.9061 (tmm) cc_final: 0.8584 (tmm) REVERT: F 255 ASN cc_start: 0.8624 (t0) cc_final: 0.8107 (m110) REVERT: G 1 MET cc_start: 0.7819 (tmm) cc_final: 0.7387 (tpt) REVERT: G 51 MET cc_start: 0.8695 (ttm) cc_final: 0.8357 (ttm) REVERT: I 40 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8453 (mt-10) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.2254 time to fit residues: 38.5008 Evaluate side-chains 106 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [129, 0, 6, 75, 60, 112, 105, 124, 101, 81, 20] chunk 129 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 overall best weight: 2.2188 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.068992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.053840 restraints weight = 145457.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.056252 restraints weight = 66714.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.057776 restraints weight = 40311.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058724 restraints weight = 29134.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.059293 restraints weight = 23737.208| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11110 Z= 0.171 Angle : 0.463 5.554 14920 Z= 0.281 Chirality : 0.029 0.113 1626 Planarity : 0.002 0.018 1924 Dihedral : 3.821 21.655 1480 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.40 (0.22), residues: 1364 helix: 2.66 (0.14), residues: 1195 sheet: None (None), residues: 0 loop : -1.04 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 19 TYR 0.022 0.001 TYR G 131 PHE 0.014 0.001 PHE F 52 TRP 0.006 0.001 TRP F 275 HIS 0.006 0.001 HIS F 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (11110) covalent geometry : angle 0.46343 / 0.28 (14920) hydrogen bonds : bond 0.05111 / 3.54 ( 926) hydrogen bonds : angle 4.03216 / 3.06 ( 2757) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.423 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: A 219 MET cc_start: 0.9234 (mtp) cc_final: 0.8874 (mtp) REVERT: A 245 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7323 (mm-30) REVERT: D 214 ASP cc_start: 0.7886 (t70) cc_final: 0.7435 (t0) REVERT: D 217 MET cc_start: 0.8928 (mmp) cc_final: 0.8712 (mmp) REVERT: E 11 MET cc_start: 0.9192 (tpp) cc_final: 0.8936 (tpp) REVERT: E 105 MET cc_start: 0.8924 (tpp) cc_final: 0.8637 (mmt) REVERT: F 23 ASN cc_start: 0.8119 (m110) cc_final: 0.7853 (m110) REVERT: F 54 MET cc_start: 0.9087 (tmm) cc_final: 0.8550 (tmm) REVERT: F 255 ASN cc_start: 0.8656 (t0) cc_final: 0.8159 (m110) REVERT: F 279 MET cc_start: 0.9545 (mmm) cc_final: 0.9087 (tpp) REVERT: G 1 MET cc_start: 0.7869 (tmm) cc_final: 0.7443 (tpt) REVERT: G 51 MET cc_start: 0.8712 (ttm) cc_final: 0.8361 (ttm) REVERT: I 40 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8456 (mt-10) REVERT: I 66 CYS cc_start: 0.9551 (t) cc_final: 0.9201 (p) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2179 time to fit residues: 36.4555 Evaluate side-chains 100 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [122, 92, 89, 30, 67, 82, 2, 93, 23, 45, 55] chunk 122 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 0.0570 chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.070554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.055218 restraints weight = 144808.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.057720 restraints weight = 66721.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059298 restraints weight = 40267.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.060276 restraints weight = 29018.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.060805 restraints weight = 23575.808| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11110 Z= 0.119 Angle : 0.435 5.665 14920 Z= 0.256 Chirality : 0.029 0.112 1626 Planarity : 0.002 0.032 1924 Dihedral : 3.714 20.995 1480 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.75 (0.22), residues: 1364 helix: 2.90 (0.14), residues: 1195 sheet: None (None), residues: 0 loop : -0.94 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.024 0.001 TYR G 131 PHE 0.014 0.001 PHE F 232 TRP 0.007 0.001 TRP I 275 HIS 0.005 0.001 HIS G 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (11110) covalent geometry : angle 0.43494 / 0.26 (14920) hydrogen bonds : bond 0.04709 / 3.26 ( 926) hydrogen bonds : angle 3.72548 / 2.83 ( 2757) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.596 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: A 219 MET cc_start: 0.9193 (mtp) cc_final: 0.8869 (mtp) REVERT: A 245 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7249 (mm-30) REVERT: D 214 ASP cc_start: 0.7974 (t70) cc_final: 0.7348 (t0) REVERT: D 217 MET cc_start: 0.8925 (mmp) cc_final: 0.8697 (mmp) REVERT: D 218 ASP cc_start: 0.8584 (m-30) cc_final: 0.7964 (m-30) REVERT: E 11 MET cc_start: 0.9197 (tpp) cc_final: 0.8943 (tpp) REVERT: F 23 ASN cc_start: 0.8098 (m110) cc_final: 0.7827 (m110) REVERT: F 54 MET cc_start: 0.9084 (tmm) cc_final: 0.8560 (tmm) REVERT: F 255 ASN cc_start: 0.8606 (t0) cc_final: 0.8118 (m110) REVERT: G 1 MET cc_start: 0.7864 (tmm) cc_final: 0.7409 (tpt) REVERT: G 51 MET cc_start: 0.8705 (ttm) cc_final: 0.8367 (ttm) REVERT: I 40 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8447 (mt-10) REVERT: I 66 CYS cc_start: 0.9510 (t) cc_final: 0.9164 (p) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2204 time to fit residues: 38.6535 Evaluate side-chains 107 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [115, 6, 106, 5, 83, 96, 130, 99, 122, 72, 33] chunk 115 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.070875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055579 restraints weight = 143337.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.058073 restraints weight = 65867.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059640 restraints weight = 39663.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060617 restraints weight = 28568.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.061217 restraints weight = 23230.787| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11110 Z= 0.111 Angle : 0.425 5.794 14920 Z= 0.250 Chirality : 0.028 0.123 1626 Planarity : 0.002 0.022 1924 Dihedral : 3.644 20.635 1480 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.88 (0.22), residues: 1364 helix: 2.99 (0.14), residues: 1195 sheet: None (None), residues: 0 loop : -0.96 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.021 0.001 TYR G 131 PHE 0.047 0.002 PHE D 216 TRP 0.008 0.001 TRP I 275 HIS 0.010 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (11110) covalent geometry : angle 0.42466 / 0.25 (14920) hydrogen bonds : bond 0.04542 / 3.15 ( 926) hydrogen bonds : angle 3.61462 / 2.74 ( 2757) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3750.10 seconds wall clock time: 64 minutes 32.53 seconds (3872.53 seconds total)