Starting phenix.real_space_refine on Thu Feb 5 01:36:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wju_66030/02_2026/9wju_66030.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wju_66030/02_2026/9wju_66030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wju_66030/02_2026/9wju_66030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wju_66030/02_2026/9wju_66030.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wju_66030/02_2026/9wju_66030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wju_66030/02_2026/9wju_66030.map" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.054 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: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 9209 2.51 5 N 2285 2.21 5 O 2464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14019 Number of models: 1 Model: "" Number of chains: 10 Chain: "Y" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1795 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 8, 'TRANS': 241} Chain: "Z" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2745 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "A" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 388 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "F" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1779 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "G" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2736 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 14, 'TRANS': 344} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1795 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 8, 'TRANS': 241} Chain: "T" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2745 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.45, per 1000 atoms: 0.25 Number of scatterers: 14019 At special positions: 0 Unit cell: (110.643, 131.052, 122.459, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 2464 8.00 N 2285 7.00 C 9209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 553.6 milliseconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3302 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 5 sheets defined 70.1% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'Y' and resid 2 through 23 removed outlier: 4.135A pdb=" N ILE Y 21 " --> pdb=" O GLY Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 41 removed outlier: 3.947A pdb=" N SER Y 35 " --> pdb=" O ILE Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 59 removed outlier: 4.363A pdb=" N GLY Y 47 " --> pdb=" O HIS Y 43 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET Y 56 " --> pdb=" O GLY Y 52 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE Y 57 " --> pdb=" O SER Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 71 through 86 removed outlier: 3.681A pdb=" N ALA Y 75 " --> pdb=" O ASP Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 92 through 97 Processing helix chain 'Y' and resid 97 through 133 removed outlier: 3.932A pdb=" N VAL Y 121 " --> pdb=" O ARG Y 117 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY Y 122 " --> pdb=" O PHE Y 118 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE Y 123 " --> pdb=" O LEU Y 119 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS Y 133 " --> pdb=" O ALA Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 164 removed outlier: 3.559A pdb=" N VAL Y 139 " --> pdb=" O SER Y 135 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE Y 154 " --> pdb=" O GLN Y 150 " (cutoff:3.500A) Proline residue: Y 157 - end of helix removed outlier: 3.877A pdb=" N ILE Y 160 " --> pdb=" O ILE Y 156 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE Y 161 " --> pdb=" O PRO Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 167 through 175 Processing helix chain 'Y' and resid 177 through 189 Processing helix chain 'Y' and resid 191 through 203 removed outlier: 3.606A pdb=" N GLY Y 195 " --> pdb=" O VAL Y 191 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET Y 198 " --> pdb=" O VAL Y 194 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL Y 199 " --> pdb=" O GLY Y 195 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET Y 203 " --> pdb=" O VAL Y 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 208 through 219 Processing helix chain 'Y' and resid 225 through 250 removed outlier: 3.744A pdb=" N ALA Y 247 " --> pdb=" O LEU Y 243 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY Y 250 " --> pdb=" O THR Y 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 11 through 23 Processing helix chain 'Z' and resid 35 through 51 removed outlier: 4.095A pdb=" N PHE Z 39 " --> pdb=" O GLN Z 35 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU Z 40 " --> pdb=" O ASN Z 36 " (cutoff:3.500A) Proline residue: Z 45 - end of helix Processing helix chain 'Z' and resid 55 through 65 removed outlier: 3.773A pdb=" N HIS Z 65 " --> pdb=" O ALA Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 92 Processing helix chain 'Z' and resid 97 through 121 removed outlier: 3.596A pdb=" N ILE Z 101 " --> pdb=" O ASP Z 97 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET Z 108 " --> pdb=" O VAL Z 104 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY Z 110 " --> pdb=" O VAL Z 106 " (cutoff:3.500A) Proline residue: Z 111 - end of helix Proline residue: Z 118 - end of helix Processing helix chain 'Z' and resid 123 through 137 removed outlier: 3.633A pdb=" N ILE Z 127 " --> pdb=" O THR Z 123 " (cutoff:3.500A) Processing helix chain 'Z' and resid 141 through 168 removed outlier: 3.821A pdb=" N ILE Z 145 " --> pdb=" O ILE Z 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 170 through 179 Processing helix chain 'Z' and resid 181 through 204 removed outlier: 4.013A pdb=" N LYS Z 187 " --> pdb=" O GLN Z 183 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 300 Processing helix chain 'Z' and resid 311 through 320 Processing helix chain 'Z' and resid 322 through 338 Processing helix chain 'Z' and resid 343 through 362 Processing helix chain 'A' and resid 26 through 43 removed outlier: 3.870A pdb=" N GLY A 43 " --> pdb=" O TRP A 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 23 removed outlier: 4.306A pdb=" N ILE F 21 " --> pdb=" O GLY F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 removed outlier: 3.911A pdb=" N SER F 35 " --> pdb=" O ILE F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 59 removed outlier: 3.884A pdb=" N MET F 56 " --> pdb=" O GLY F 52 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE F 57 " --> pdb=" O SER F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 86 removed outlier: 3.693A pdb=" N ALA F 75 " --> pdb=" O ASP F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 97 through 132 removed outlier: 3.861A pdb=" N VAL F 121 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 164 removed outlier: 3.603A pdb=" N VAL F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE F 154 " --> pdb=" O GLN F 150 " (cutoff:3.500A) Proline residue: F 157 - end of helix removed outlier: 3.745A pdb=" N ILE F 164 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 175 removed outlier: 3.565A pdb=" N VAL F 169 " --> pdb=" O PRO F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 188 Processing helix chain 'F' and resid 190 through 203 removed outlier: 4.247A pdb=" N VAL F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY F 195 " --> pdb=" O VAL F 191 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL F 199 " --> pdb=" O GLY F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 219 removed outlier: 4.214A pdb=" N PHE F 212 " --> pdb=" O LEU F 208 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE F 213 " --> pdb=" O TRP F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 246 removed outlier: 3.556A pdb=" N THR F 246 " --> pdb=" O ASN F 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 23 removed outlier: 3.582A pdb=" N ARG G 15 " --> pdb=" O SER G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 51 removed outlier: 3.627A pdb=" N LEU G 40 " --> pdb=" O ASN G 36 " (cutoff:3.500A) Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 55 through 65 Processing helix chain 'G' and resid 76 through 91 Processing helix chain 'G' and resid 99 through 107 Processing helix chain 'G' and resid 108 through 122 Proline residue: G 118 - end of helix Processing helix chain 'G' and resid 123 through 137 Processing helix chain 'G' and resid 141 through 170 removed outlier: 3.640A pdb=" N ILE G 145 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU G 164 " --> pdb=" O TRP G 160 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN G 169 " --> pdb=" O PHE G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 180 through 204 removed outlier: 3.756A pdb=" N ILE G 185 " --> pdb=" O MET G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 283 removed outlier: 3.763A pdb=" N GLN G 282 " --> pdb=" O THR G 279 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G 283 " --> pdb=" O VAL G 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 279 through 283' Processing helix chain 'G' and resid 288 through 300 removed outlier: 3.850A pdb=" N HIS G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 320 Processing helix chain 'G' and resid 322 through 340 removed outlier: 3.808A pdb=" N LYS G 340 " --> pdb=" O LEU G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 362 removed outlier: 3.653A pdb=" N PHE G 347 " --> pdb=" O ASN G 343 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 20 Processing helix chain 'S' and resid 29 through 41 removed outlier: 4.063A pdb=" N SER S 35 " --> pdb=" O ILE S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 58 removed outlier: 3.885A pdb=" N MET S 56 " --> pdb=" O GLY S 52 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE S 57 " --> pdb=" O SER S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 86 removed outlier: 3.892A pdb=" N ALA S 75 " --> pdb=" O ASP S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 97 removed outlier: 3.962A pdb=" N THR S 95 " --> pdb=" O LEU S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 132 removed outlier: 3.586A pdb=" N LEU S 115 " --> pdb=" O VAL S 111 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL S 121 " --> pdb=" O ARG S 117 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY S 122 " --> pdb=" O PHE S 118 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE S 123 " --> pdb=" O LEU S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 164 removed outlier: 3.911A pdb=" N VAL S 139 " --> pdb=" O SER S 135 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE S 154 " --> pdb=" O GLN S 150 " (cutoff:3.500A) Proline residue: S 157 - end of helix removed outlier: 3.812A pdb=" N ILE S 164 " --> pdb=" O ILE S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 174 removed outlier: 3.525A pdb=" N VAL S 169 " --> pdb=" O PRO S 165 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 189 Processing helix chain 'S' and resid 191 through 203 removed outlier: 3.766A pdb=" N GLY S 195 " --> pdb=" O VAL S 191 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET S 198 " --> pdb=" O VAL S 194 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL S 199 " --> pdb=" O GLY S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 219 removed outlier: 3.914A pdb=" N PHE S 212 " --> pdb=" O LEU S 208 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE S 213 " --> pdb=" O TRP S 209 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 250 Processing helix chain 'T' and resid 11 through 23 Processing helix chain 'T' and resid 35 through 43 removed outlier: 4.115A pdb=" N PHE T 39 " --> pdb=" O GLN T 35 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 49 removed outlier: 3.719A pdb=" N LEU T 47 " --> pdb=" O ILE T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 64 Processing helix chain 'T' and resid 76 through 91 Processing helix chain 'T' and resid 97 through 121 removed outlier: 4.493A pdb=" N ILE T 101 " --> pdb=" O ASP T 97 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN T 102 " --> pdb=" O GLU T 98 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY T 110 " --> pdb=" O VAL T 106 " (cutoff:3.500A) Proline residue: T 111 - end of helix Proline residue: T 118 - end of helix Processing helix chain 'T' and resid 123 through 137 removed outlier: 3.665A pdb=" N ILE T 127 " --> pdb=" O THR T 123 " (cutoff:3.500A) Processing helix chain 'T' and resid 141 through 170 removed outlier: 4.103A pdb=" N ILE T 145 " --> pdb=" O ILE T 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 172 through 178 Processing helix chain 'T' and resid 180 through 204 removed outlier: 3.632A pdb=" N GLN T 184 " --> pdb=" O GLY T 180 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE T 185 " --> pdb=" O MET T 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 288 through 300 removed outlier: 4.000A pdb=" N HIS T 292 " --> pdb=" O GLY T 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 320 Processing helix chain 'T' and resid 322 through 339 Processing helix chain 'T' and resid 343 through 363 removed outlier: 3.584A pdb=" N PHE T 347 " --> pdb=" O ASN T 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 267 through 268 removed outlier: 8.375A pdb=" N LYS Z 253 " --> pdb=" O GLN Z 243 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN Z 243 " --> pdb=" O LYS Z 253 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP Z 255 " --> pdb=" O GLY Z 241 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP Z 230 " --> pdb=" O VAL Z 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.516A pdb=" N THR A 13 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 20 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 263 through 264 removed outlier: 3.524A pdb=" N TRP G 256 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LYS G 253 " --> pdb=" O THR G 244 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA G 242 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU G 257 " --> pdb=" O GLN G 240 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLN G 240 " --> pdb=" O LEU G 257 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP G 230 " --> pdb=" O VAL G 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 229 through 231 Processing sheet with id=AA5, first strand: chain 'T' and resid 239 through 246 removed outlier: 4.696A pdb=" N ASP T 255 " --> pdb=" O GLY T 241 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN T 243 " --> pdb=" O LYS T 253 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LYS T 253 " --> pdb=" O GLN T 243 " (cutoff:3.500A) 907 hydrogen bonds defined for protein. 2697 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: 2.39 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4329 1.34 - 1.46: 2446 1.46 - 1.58: 7441 1.58 - 1.70: 2 1.70 - 1.82: 119 Bond restraints: 14337 Sorted by residual: bond pdb=" CG PRO Z 212 " pdb=" CD PRO Z 212 " ideal model delta sigma weight residual 1.503 1.361 0.142 3.40e-02 8.65e+02 1.75e+01 bond pdb=" CB PRO Z 212 " pdb=" CG PRO Z 212 " ideal model delta sigma weight residual 1.492 1.581 -0.089 5.00e-02 4.00e+02 3.19e+00 bond pdb=" C5 MAN G 401 " pdb=" O5 MAN G 401 " ideal model delta sigma weight residual 1.418 1.453 -0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" CB PRO G 220 " pdb=" CG PRO G 220 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.08e+00 bond pdb=" CG1 ILE F 39 " pdb=" CD1 ILE F 39 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.45e+00 ... (remaining 14332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 19301 2.79 - 5.58: 186 5.58 - 8.38: 21 8.38 - 11.17: 11 11.17 - 13.96: 5 Bond angle restraints: 19524 Sorted by residual: angle pdb=" N PRO Z 212 " pdb=" CD PRO Z 212 " pdb=" CG PRO Z 212 " ideal model delta sigma weight residual 103.20 91.79 11.41 1.50e+00 4.44e-01 5.79e+01 angle pdb=" CA PRO Z 212 " pdb=" N PRO Z 212 " pdb=" CD PRO Z 212 " ideal model delta sigma weight residual 112.00 103.72 8.28 1.40e+00 5.10e-01 3.49e+01 angle pdb=" C LEU Z 221 " pdb=" CA LEU Z 221 " pdb=" CB LEU Z 221 " ideal model delta sigma weight residual 117.23 110.48 6.75 1.36e+00 5.41e-01 2.46e+01 angle pdb=" CA LEU F 15 " pdb=" CB LEU F 15 " pdb=" CG LEU F 15 " ideal model delta sigma weight residual 116.30 130.26 -13.96 3.50e+00 8.16e-02 1.59e+01 angle pdb=" CA LEU F 238 " pdb=" CB LEU F 238 " pdb=" CG LEU F 238 " ideal model delta sigma weight residual 116.30 130.22 -13.92 3.50e+00 8.16e-02 1.58e+01 ... (remaining 19519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.51: 7437 23.51 - 47.02: 685 47.02 - 70.52: 99 70.52 - 94.03: 27 94.03 - 117.54: 2 Dihedral angle restraints: 8250 sinusoidal: 3041 harmonic: 5209 Sorted by residual: dihedral pdb=" CA ILE Y 164 " pdb=" C ILE Y 164 " pdb=" N PRO Y 165 " pdb=" CA PRO Y 165 " ideal model delta harmonic sigma weight residual 180.00 140.59 39.41 0 5.00e+00 4.00e-02 6.21e+01 dihedral pdb=" C2 MAN G 401 " pdb=" C1 MAN G 401 " pdb=" O5 MAN G 401 " pdb=" C5 MAN G 401 " ideal model delta sinusoidal sigma weight residual -57.62 59.92 -117.54 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" C5 MAN G 401 " pdb=" C1 MAN G 401 " pdb=" O5 MAN G 401 " pdb=" O1 MAN G 401 " ideal model delta sinusoidal sigma weight residual -63.34 -179.54 116.20 1 3.00e+01 1.11e-03 1.54e+01 ... (remaining 8247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1829 0.050 - 0.100: 409 0.100 - 0.150: 76 0.150 - 0.200: 2 0.200 - 0.250: 3 Chirality restraints: 2319 Sorted by residual: chirality pdb=" CG LEU F 126 " pdb=" CB LEU F 126 " pdb=" CD1 LEU F 126 " pdb=" CD2 LEU F 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CG LEU S 36 " pdb=" CB LEU S 36 " pdb=" CD1 LEU S 36 " pdb=" CD2 LEU S 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE F 21 " pdb=" CA ILE F 21 " pdb=" CG1 ILE F 21 " pdb=" CG2 ILE F 21 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2316 not shown) Planarity restraints: 2427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE Y 164 " -0.104 5.00e-02 4.00e+02 1.57e-01 3.96e+01 pdb=" N PRO Y 165 " 0.272 5.00e-02 4.00e+02 pdb=" CA PRO Y 165 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO Y 165 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 219 " 0.071 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO G 220 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO G 220 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO G 220 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 26 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO A 27 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.030 5.00e-02 4.00e+02 ... (remaining 2424 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 397 2.70 - 3.25: 15382 3.25 - 3.80: 23658 3.80 - 4.35: 28475 4.35 - 4.90: 47004 Nonbonded interactions: 114916 Sorted by model distance: nonbonded pdb=" O PRO T 118 " pdb=" OG1 THR T 123 " model vdw 2.151 3.040 nonbonded pdb=" O SER T 11 " pdb=" OG1 THR T 14 " model vdw 2.194 3.040 nonbonded pdb=" O ASP Z 287 " pdb=" OG1 THR Z 290 " model vdw 2.208 3.040 nonbonded pdb=" O PHE Z 158 " pdb=" OG1 THR Z 162 " model vdw 2.208 3.040 nonbonded pdb=" O LEU Z 10 " pdb=" NH2 ARG Z 15 " model vdw 2.209 3.120 ... (remaining 114911 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 'F' selection = (chain 'S' and resid 1 through 247) selection = (chain 'Y' and resid 1 through 247) } ncs_group { reference = chain 'G' selection = (chain 'T' and resid 7 through 401) selection = (chain 'Z' and resid 7 through 401) } 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=1.00 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: 1.340 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.150 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 0.142 14337 Z= 0.166 Angle : 0.736 13.960 19524 Z= 0.364 Chirality : 0.042 0.250 2319 Planarity : 0.006 0.157 2427 Dihedral : 17.882 117.538 4948 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.41 % Favored : 92.38 % Rotamer: Outliers : 0.35 % Allowed : 34.10 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.20), residues: 1863 helix: 1.21 (0.15), residues: 1219 sheet: -1.12 (1.03), residues: 30 loop : -2.03 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 153 TYR 0.015 0.001 TYR Y 240 PHE 0.028 0.001 PHE Y 12 TRP 0.024 0.001 TRP Y 179 HIS 0.005 0.001 HIS Z 360 Details of bonding type rmsd covalent geometry : bond 0.00402 (14337) covalent geometry : angle 0.73559 (19524) hydrogen bonds : bond 0.11404 ( 907) hydrogen bonds : angle 5.54022 ( 2697) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 247 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: Z 62 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8802 (mm) REVERT: G 353 PHE cc_start: 0.8504 (m-80) cc_final: 0.8304 (m-80) REVERT: T 34 MET cc_start: 0.3648 (mmm) cc_final: 0.3286 (mmm) outliers start: 5 outliers final: 1 residues processed: 250 average time/residue: 0.0956 time to fit residues: 37.7564 Evaluate side-chains 239 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 237 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 62 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN T 202 GLN ** T 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.128385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100559 restraints weight = 32431.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.103133 restraints weight = 16538.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104709 restraints weight = 10729.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105605 restraints weight = 8225.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106252 restraints weight = 7079.726| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 14337 Z= 0.211 Angle : 0.670 10.057 19524 Z= 0.340 Chirality : 0.043 0.182 2319 Planarity : 0.006 0.156 2427 Dihedral : 4.795 36.399 2009 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.25 % Favored : 92.54 % Rotamer: Outliers : 5.80 % Allowed : 28.09 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1863 helix: 1.23 (0.15), residues: 1237 sheet: -1.20 (0.99), residues: 30 loop : -2.22 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 153 TYR 0.017 0.002 TYR S 196 PHE 0.017 0.001 PHE Y 12 TRP 0.024 0.001 TRP Y 179 HIS 0.006 0.001 HIS A 3 Details of bonding type rmsd covalent geometry : bond 0.00500 (14337) covalent geometry : angle 0.67048 (19524) hydrogen bonds : bond 0.04461 ( 907) hydrogen bonds : angle 4.75484 ( 2697) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 239 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: Z 32 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7842 (pp20) REVERT: Z 223 ASP cc_start: 0.7207 (t0) cc_final: 0.6964 (t0) REVERT: A 1 GLU cc_start: 0.8535 (pm20) cc_final: 0.8286 (pm20) REVERT: F 89 PHE cc_start: 0.6601 (OUTLIER) cc_final: 0.5841 (m-80) REVERT: G 19 MET cc_start: 0.8488 (tpp) cc_final: 0.8116 (tpp) REVERT: G 34 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.5611 (mtt) REVERT: G 98 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7300 (pp20) REVERT: G 164 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6234 (mt-10) REVERT: G 342 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6911 (mtpt) REVERT: S 6 ILE cc_start: 0.6080 (OUTLIER) cc_final: 0.5692 (mp) REVERT: S 24 GLN cc_start: 0.8366 (mp10) cc_final: 0.8144 (mp10) REVERT: T 125 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8224 (tpt-90) outliers start: 83 outliers final: 37 residues processed: 307 average time/residue: 0.0993 time to fit residues: 47.7742 Evaluate side-chains 268 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Y residue 179 TRP Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 12 LYS Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 32 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 109 MET Chi-restraints excluded: chain Z residue 149 VAL Chi-restraints excluded: chain Z residue 218 SER Chi-restraints excluded: chain Z residue 221 LEU Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 286 VAL Chi-restraints excluded: chain Z residue 324 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain G residue 342 LYS Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 190 MET Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain T residue 125 ARG Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 320 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 2 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.099755 restraints weight = 32738.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.102274 restraints weight = 16975.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103796 restraints weight = 11030.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104774 restraints weight = 8481.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.105240 restraints weight = 7274.906| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14337 Z= 0.202 Angle : 0.665 11.226 19524 Z= 0.336 Chirality : 0.043 0.222 2319 Planarity : 0.006 0.157 2427 Dihedral : 4.541 39.734 2005 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.09 % Favored : 92.70 % Rotamer: Outliers : 5.38 % Allowed : 28.79 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.20), residues: 1863 helix: 1.25 (0.15), residues: 1237 sheet: -1.25 (0.98), residues: 30 loop : -2.28 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 153 TYR 0.018 0.002 TYR S 196 PHE 0.020 0.001 PHE Y 12 TRP 0.023 0.001 TRP Y 179 HIS 0.006 0.001 HIS Z 360 Details of bonding type rmsd covalent geometry : bond 0.00481 (14337) covalent geometry : angle 0.66508 (19524) hydrogen bonds : bond 0.04287 ( 907) hydrogen bonds : angle 4.70935 ( 2697) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 239 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: Y 89 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: Y 150 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7531 (tm-30) REVERT: Z 135 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9172 (mm) REVERT: F 89 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.5937 (m-80) REVERT: F 203 MET cc_start: 0.9030 (pmm) cc_final: 0.8614 (pmm) REVERT: G 19 MET cc_start: 0.8539 (tpp) cc_final: 0.8065 (tpp) REVERT: G 98 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7355 (pp20) REVERT: G 164 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6185 (mt-10) REVERT: G 342 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6882 (mtpt) REVERT: S 6 ILE cc_start: 0.6069 (OUTLIER) cc_final: 0.5680 (mp) REVERT: S 29 GLN cc_start: 0.7679 (mm110) cc_final: 0.7444 (mm-40) REVERT: S 59 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8659 (mm) REVERT: T 125 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8219 (tpt-90) REVERT: T 181 MET cc_start: 0.8073 (tpp) cc_final: 0.7833 (tpp) REVERT: T 223 ASP cc_start: 0.7181 (t0) cc_final: 0.6810 (t0) outliers start: 77 outliers final: 42 residues processed: 300 average time/residue: 0.0981 time to fit residues: 47.2015 Evaluate side-chains 268 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 89 PHE Chi-restraints excluded: chain Y residue 111 VAL Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Y residue 179 TRP Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 18 VAL Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 109 MET Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 135 LEU Chi-restraints excluded: chain Z residue 145 ILE Chi-restraints excluded: chain Z residue 177 LEU Chi-restraints excluded: chain Z residue 218 SER Chi-restraints excluded: chain Z residue 264 VAL Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 324 ILE Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain G residue 342 LYS Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 190 MET Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 242 ASN Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 125 ARG Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 320 ILE Chi-restraints excluded: chain T residue 324 ILE Chi-restraints excluded: chain T residue 359 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 135 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN ** T 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.130005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.102785 restraints weight = 32305.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.105379 restraints weight = 16372.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106965 restraints weight = 10537.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107950 restraints weight = 8064.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108451 restraints weight = 6895.242| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14337 Z= 0.137 Angle : 0.621 11.904 19524 Z= 0.310 Chirality : 0.042 0.234 2319 Planarity : 0.006 0.152 2427 Dihedral : 4.451 36.987 2005 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.76 % Favored : 93.02 % Rotamer: Outliers : 5.38 % Allowed : 28.93 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1863 helix: 1.37 (0.15), residues: 1238 sheet: -1.34 (0.97), residues: 30 loop : -2.24 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 153 TYR 0.022 0.001 TYR S 196 PHE 0.019 0.001 PHE Y 12 TRP 0.021 0.001 TRP Y 179 HIS 0.005 0.001 HIS Z 360 Details of bonding type rmsd covalent geometry : bond 0.00318 (14337) covalent geometry : angle 0.62133 (19524) hydrogen bonds : bond 0.03898 ( 907) hydrogen bonds : angle 4.50897 ( 2697) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 245 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: Y 89 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7995 (m-80) REVERT: Y 150 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7650 (tm-30) REVERT: Z 23 MET cc_start: 0.8196 (mmt) cc_final: 0.7663 (mmm) REVERT: Z 32 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7760 (pp20) REVERT: Z 62 LEU cc_start: 0.8675 (mm) cc_final: 0.8423 (mm) REVERT: Z 223 ASP cc_start: 0.7279 (t0) cc_final: 0.6942 (t0) REVERT: F 89 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.5853 (m-80) REVERT: F 203 MET cc_start: 0.8947 (pmm) cc_final: 0.8521 (pmm) REVERT: G 26 GLN cc_start: 0.6787 (mt0) cc_final: 0.6337 (mt0) REVERT: G 79 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8357 (mt) REVERT: G 98 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7283 (pp20) REVERT: G 164 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6105 (mt-10) REVERT: S 6 ILE cc_start: 0.6046 (OUTLIER) cc_final: 0.5638 (mp) REVERT: S 59 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8562 (mm) REVERT: T 181 MET cc_start: 0.8008 (tpp) cc_final: 0.7793 (tpp) REVERT: T 223 ASP cc_start: 0.7180 (t0) cc_final: 0.6698 (t0) outliers start: 77 outliers final: 43 residues processed: 308 average time/residue: 0.0949 time to fit residues: 46.7378 Evaluate side-chains 277 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 89 PHE Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Y residue 169 VAL Chi-restraints excluded: chain Y residue 179 TRP Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 32 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 109 MET Chi-restraints excluded: chain Z residue 145 ILE Chi-restraints excluded: chain Z residue 177 LEU Chi-restraints excluded: chain Z residue 218 SER Chi-restraints excluded: chain Z residue 264 VAL Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 319 LEU Chi-restraints excluded: chain Z residue 324 ILE Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 174 ASN Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 235 VAL Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 182 LEU Chi-restraints excluded: chain T residue 320 ILE Chi-restraints excluded: chain T residue 324 ILE Chi-restraints excluded: chain T residue 352 MET Chi-restraints excluded: chain T residue 359 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 151 optimal weight: 0.1980 chunk 111 optimal weight: 20.0000 chunk 146 optimal weight: 0.5980 chunk 125 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.129625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102126 restraints weight = 32366.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104702 restraints weight = 16576.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106241 restraints weight = 10734.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107222 restraints weight = 8271.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107705 restraints weight = 7082.730| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14337 Z= 0.142 Angle : 0.629 12.059 19524 Z= 0.314 Chirality : 0.042 0.244 2319 Planarity : 0.006 0.148 2427 Dihedral : 4.393 34.369 2005 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.09 % Favored : 92.75 % Rotamer: Outliers : 5.66 % Allowed : 29.63 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1863 helix: 1.34 (0.15), residues: 1238 sheet: -1.38 (0.98), residues: 30 loop : -2.23 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 153 TYR 0.021 0.001 TYR S 196 PHE 0.021 0.001 PHE S 12 TRP 0.021 0.001 TRP Y 179 HIS 0.006 0.001 HIS S 93 Details of bonding type rmsd covalent geometry : bond 0.00336 (14337) covalent geometry : angle 0.62947 (19524) hydrogen bonds : bond 0.03871 ( 907) hydrogen bonds : angle 4.47075 ( 2697) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 241 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: Y 89 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7937 (m-80) REVERT: Y 150 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7676 (tm-30) REVERT: Z 32 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7765 (pp20) REVERT: Z 62 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8091 (mm) REVERT: Z 135 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9112 (mm) REVERT: F 89 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.5942 (m-80) REVERT: F 203 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8503 (pmm) REVERT: G 19 MET cc_start: 0.8479 (tpp) cc_final: 0.8270 (ttm) REVERT: G 86 LEU cc_start: 0.9187 (tp) cc_final: 0.8942 (tp) REVERT: G 98 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7274 (pp20) REVERT: G 164 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6123 (mt-10) REVERT: S 6 ILE cc_start: 0.6111 (OUTLIER) cc_final: 0.5657 (mp) REVERT: S 27 PHE cc_start: 0.6766 (m-80) cc_final: 0.6555 (m-80) REVERT: S 59 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8474 (mm) REVERT: S 196 TYR cc_start: 0.9224 (m-80) cc_final: 0.9011 (m-80) REVERT: T 125 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8124 (tpt-90) REVERT: T 181 MET cc_start: 0.8034 (tpp) cc_final: 0.7808 (tpp) REVERT: T 223 ASP cc_start: 0.7222 (t0) cc_final: 0.6747 (t0) REVERT: T 226 TYR cc_start: 0.8171 (p90) cc_final: 0.7731 (p90) REVERT: T 236 LYS cc_start: 0.8408 (tppt) cc_final: 0.8194 (tppt) REVERT: T 352 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7774 (ttt) outliers start: 81 outliers final: 49 residues processed: 302 average time/residue: 0.0951 time to fit residues: 45.8572 Evaluate side-chains 285 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 224 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 89 PHE Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Y residue 111 VAL Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Y residue 169 VAL Chi-restraints excluded: chain Y residue 170 THR Chi-restraints excluded: chain Y residue 179 TRP Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 32 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 62 LEU Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 135 LEU Chi-restraints excluded: chain Z residue 145 ILE Chi-restraints excluded: chain Z residue 177 LEU Chi-restraints excluded: chain Z residue 218 SER Chi-restraints excluded: chain Z residue 264 VAL Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 319 LEU Chi-restraints excluded: chain Z residue 324 ILE Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain T residue 125 ARG Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 290 THR Chi-restraints excluded: chain T residue 320 ILE Chi-restraints excluded: chain T residue 324 ILE Chi-restraints excluded: chain T residue 352 MET Chi-restraints excluded: chain T residue 359 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 104 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN ** S 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.130032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102649 restraints weight = 32279.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105250 restraints weight = 16504.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106816 restraints weight = 10650.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107779 restraints weight = 8139.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.108291 restraints weight = 6982.925| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14337 Z= 0.137 Angle : 0.634 12.376 19524 Z= 0.316 Chirality : 0.042 0.236 2319 Planarity : 0.006 0.154 2427 Dihedral : 4.355 36.505 2005 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.98 % Favored : 92.86 % Rotamer: Outliers : 6.29 % Allowed : 29.14 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1863 helix: 1.32 (0.15), residues: 1240 sheet: -1.43 (0.96), residues: 30 loop : -2.17 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 153 TYR 0.018 0.001 TYR S 196 PHE 0.013 0.001 PHE T 158 TRP 0.021 0.001 TRP Y 179 HIS 0.005 0.001 HIS Z 360 Details of bonding type rmsd covalent geometry : bond 0.00318 (14337) covalent geometry : angle 0.63434 (19524) hydrogen bonds : bond 0.03782 ( 907) hydrogen bonds : angle 4.43626 ( 2697) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 247 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 150 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7696 (tm-30) REVERT: Z 32 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7750 (pp20) REVERT: Z 62 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8416 (mm) REVERT: Z 135 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9089 (mm) REVERT: Z 223 ASP cc_start: 0.7379 (t0) cc_final: 0.7032 (t0) REVERT: F 89 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.5926 (m-80) REVERT: F 203 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8494 (pmm) REVERT: G 19 MET cc_start: 0.8436 (tpp) cc_final: 0.8076 (tpp) REVERT: G 26 GLN cc_start: 0.6651 (mt0) cc_final: 0.6406 (mt0) REVERT: G 98 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7198 (pp20) REVERT: G 164 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6118 (mt-10) REVERT: G 181 MET cc_start: 0.8281 (tmm) cc_final: 0.7928 (tmm) REVERT: G 342 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6810 (mtpt) REVERT: S 6 ILE cc_start: 0.6148 (OUTLIER) cc_final: 0.5712 (mp) REVERT: S 59 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8534 (mm) REVERT: T 40 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7556 (tt) REVERT: T 125 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8161 (tpt-90) REVERT: T 181 MET cc_start: 0.8020 (tpp) cc_final: 0.7808 (tpp) REVERT: T 223 ASP cc_start: 0.7328 (t0) cc_final: 0.6883 (t0) REVERT: T 226 TYR cc_start: 0.8182 (p90) cc_final: 0.7739 (p90) REVERT: T 352 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7803 (ttt) outliers start: 90 outliers final: 56 residues processed: 316 average time/residue: 0.0969 time to fit residues: 49.0362 Evaluate side-chains 301 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 232 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Y residue 111 VAL Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Y residue 169 VAL Chi-restraints excluded: chain Y residue 170 THR Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 32 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 62 LEU Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 135 LEU Chi-restraints excluded: chain Z residue 145 ILE Chi-restraints excluded: chain Z residue 177 LEU Chi-restraints excluded: chain Z residue 218 SER Chi-restraints excluded: chain Z residue 221 LEU Chi-restraints excluded: chain Z residue 264 VAL Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 319 LEU Chi-restraints excluded: chain Z residue 324 ILE Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 93 HIS Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 207 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 342 LYS Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 174 ASN Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 242 ASN Chi-restraints excluded: chain T residue 20 PHE Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain T residue 125 ARG Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 290 THR Chi-restraints excluded: chain T residue 320 ILE Chi-restraints excluded: chain T residue 324 ILE Chi-restraints excluded: chain T residue 346 LEU Chi-restraints excluded: chain T residue 352 MET Chi-restraints excluded: chain T residue 359 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 88 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 177 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.131723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.104500 restraints weight = 31978.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107109 restraints weight = 16324.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108723 restraints weight = 10529.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109556 restraints weight = 8050.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110170 restraints weight = 6946.799| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14337 Z= 0.125 Angle : 0.641 12.979 19524 Z= 0.315 Chirality : 0.041 0.260 2319 Planarity : 0.006 0.153 2427 Dihedral : 4.286 36.066 2005 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.60 % Favored : 93.24 % Rotamer: Outliers : 5.10 % Allowed : 31.17 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1863 helix: 1.32 (0.15), residues: 1242 sheet: -1.43 (0.96), residues: 30 loop : -2.16 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 153 TYR 0.014 0.001 TYR Y 240 PHE 0.016 0.001 PHE S 27 TRP 0.019 0.001 TRP Y 179 HIS 0.005 0.001 HIS T 360 Details of bonding type rmsd covalent geometry : bond 0.00280 (14337) covalent geometry : angle 0.64065 (19524) hydrogen bonds : bond 0.03629 ( 907) hydrogen bonds : angle 4.37048 ( 2697) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 254 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 89 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: Y 150 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7659 (tm-30) REVERT: Z 19 MET cc_start: 0.8036 (tmm) cc_final: 0.7783 (tmm) REVERT: Z 32 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7680 (pp20) REVERT: Z 287 ASP cc_start: 0.8017 (p0) cc_final: 0.7787 (p0) REVERT: Z 324 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9046 (mp) REVERT: F 89 PHE cc_start: 0.6459 (OUTLIER) cc_final: 0.5811 (m-80) REVERT: F 203 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8488 (pmm) REVERT: G 19 MET cc_start: 0.8407 (tpp) cc_final: 0.8045 (tpp) REVERT: G 164 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.5989 (mt-10) REVERT: G 169 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6612 (tm-30) REVERT: S 6 ILE cc_start: 0.6118 (OUTLIER) cc_final: 0.5658 (mp) REVERT: S 59 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8510 (mm) REVERT: T 40 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7630 (tt) REVERT: T 223 ASP cc_start: 0.7237 (t0) cc_final: 0.6776 (t0) REVERT: T 226 TYR cc_start: 0.8158 (p90) cc_final: 0.7680 (p90) REVERT: T 236 LYS cc_start: 0.8374 (tppt) cc_final: 0.8116 (tppt) REVERT: T 360 HIS cc_start: 0.8001 (t70) cc_final: 0.7681 (t70) outliers start: 73 outliers final: 49 residues processed: 307 average time/residue: 0.0856 time to fit residues: 42.1925 Evaluate side-chains 297 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 238 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 89 PHE Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Y residue 111 VAL Chi-restraints excluded: chain Y residue 139 VAL Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Y residue 169 VAL Chi-restraints excluded: chain Y residue 170 THR Chi-restraints excluded: chain Y residue 179 TRP Chi-restraints excluded: chain Y residue 199 VAL Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 226 LEU Chi-restraints excluded: chain Z residue 32 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 145 ILE Chi-restraints excluded: chain Z residue 177 LEU Chi-restraints excluded: chain Z residue 218 SER Chi-restraints excluded: chain Z residue 264 VAL Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 319 LEU Chi-restraints excluded: chain Z residue 324 ILE Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 169 GLN Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 281 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 352 MET Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 62 LEU Chi-restraints excluded: chain T residue 86 LEU Chi-restraints excluded: chain T residue 112 LEU Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 290 THR Chi-restraints excluded: chain T residue 346 LEU Chi-restraints excluded: chain T residue 352 MET Chi-restraints excluded: chain T residue 359 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.4243 > 50: distance: 55 - 57: 20.940 distance: 57 - 58: 38.989 distance: 58 - 59: 45.323 distance: 58 - 61: 12.207 distance: 59 - 60: 36.725 distance: 59 - 63: 41.681 distance: 60 - 86: 13.185 distance: 61 - 62: 42.367 distance: 63 - 64: 39.025 distance: 64 - 65: 59.628 distance: 64 - 67: 47.960 distance: 65 - 66: 47.996 distance: 65 - 72: 48.978 distance: 66 - 95: 42.569 distance: 67 - 68: 32.472 distance: 68 - 69: 11.783 distance: 69 - 70: 14.422 distance: 69 - 71: 5.700 distance: 72 - 73: 50.198 distance: 73 - 74: 64.424 distance: 73 - 76: 44.628 distance: 74 - 75: 59.017 distance: 74 - 81: 58.923 distance: 75 - 104: 28.583 distance: 76 - 77: 20.280 distance: 77 - 78: 3.339 distance: 78 - 79: 7.753 distance: 78 - 80: 11.313 distance: 81 - 82: 54.813 distance: 82 - 83: 54.631 distance: 82 - 85: 31.646 distance: 83 - 84: 30.455 distance: 83 - 86: 51.540 distance: 84 - 109: 14.966 distance: 86 - 87: 39.954 distance: 87 - 88: 43.517 distance: 87 - 90: 13.419 distance: 88 - 89: 39.408 distance: 88 - 95: 50.035 distance: 89 - 117: 23.724 distance: 90 - 91: 19.690 distance: 91 - 92: 26.370 distance: 92 - 93: 13.163 distance: 93 - 94: 14.678 distance: 95 - 96: 26.239 distance: 96 - 97: 54.142 distance: 96 - 99: 36.948 distance: 97 - 98: 38.340 distance: 97 - 104: 42.414 distance: 98 - 126: 40.047 distance: 99 - 100: 13.473 distance: 100 - 101: 9.059 distance: 101 - 102: 15.460 distance: 101 - 103: 19.572 distance: 104 - 105: 28.183 distance: 105 - 106: 48.493 distance: 105 - 108: 46.058 distance: 106 - 107: 53.314 distance: 106 - 109: 37.318 distance: 109 - 110: 38.765 distance: 110 - 111: 60.932 distance: 110 - 113: 20.517 distance: 111 - 112: 43.554 distance: 111 - 117: 40.907 distance: 113 - 114: 27.369 distance: 114 - 115: 31.925 distance: 114 - 116: 31.858 distance: 117 - 118: 36.555 distance: 118 - 119: 17.949 distance: 118 - 121: 34.643 distance: 119 - 120: 45.048 distance: 119 - 126: 44.818 distance: 121 - 122: 30.635 distance: 122 - 123: 14.804 distance: 123 - 124: 26.586 distance: 124 - 125: 28.851 distance: 126 - 127: 30.067 distance: 127 - 128: 18.120 distance: 127 - 130: 55.888 distance: 128 - 129: 18.847 distance: 128 - 137: 12.867 distance: 130 - 131: 21.454 distance: 131 - 132: 15.221 distance: 132 - 133: 6.386 distance: 133 - 134: 6.869 distance: 134 - 135: 15.256 distance: 134 - 136: 17.967