Starting phenix.real_space_refine on Sun Jul 5 15:00:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lnc_0930/07_2026/6lnc_0930.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lnc_0930/07_2026/6lnc_0930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lnc_0930/07_2026/6lnc_0930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lnc_0930/07_2026/6lnc_0930.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6lnc_0930/07_2026/6lnc_0930.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lnc_0930/07_2026/6lnc_0930.cif" model { file = "/net/cci-nas-00/data/ceres_data/6lnc_0930/07_2026/6lnc_0930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lnc_0930/07_2026/6lnc_0930.cif" } resolution = 3.21 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 151 5.16 5 C 18194 2.51 5 N 4991 2.21 5 O 5542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28937 Number of models: 1 Model: "" Number of chains: 11 Chain: "M" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1276 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 13, 'rna3p_pur': 22, 'rna3p_pyr': 17} Link IDs: {'rna2p': 21, 'rna3p': 38} Chain: "G" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2697 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 319} Chain breaks: 2 Chain: "F" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2688 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain breaks: 2 Chain: "E" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2689 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2697 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2682 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2500 Classifications: {'peptide': 309} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 292} Chain breaks: 2 Chain: "H" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3957 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 479} Chain breaks: 3 Chain: "A" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1611 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "J" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3070 Classifications: {'peptide': 376} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 357} Chain breaks: 2 Chain: "I" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3070 Classifications: {'peptide': 376} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 357} Chain breaks: 2 Time building chain proxies: 5.90, per 1000 atoms: 0.20 Number of scatterers: 28937 At special positions: 0 Unit cell: (149.04, 170.64, 179.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 151 16.00 P 59 15.00 O 5542 8.00 N 4991 7.00 C 18194 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: 2.27 Conformation dependent library (CDL) restraints added in 1.2 seconds 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6562 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 37 sheets defined 29.3% alpha, 13.8% beta 6 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'G' and resid 106 through 123 Processing helix chain 'G' and resid 125 through 134 removed outlier: 3.782A pdb=" N MET G 134 " --> pdb=" O THR G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 183 Processing helix chain 'G' and resid 186 through 200 removed outlier: 3.960A pdb=" N ILE G 190 " --> pdb=" O ASN G 186 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE G 194 " --> pdb=" O ILE G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 269 removed outlier: 3.549A pdb=" N ALA G 266 " --> pdb=" O PHE G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 310 removed outlier: 3.641A pdb=" N ILE G 309 " --> pdb=" O ASP G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 320 removed outlier: 3.804A pdb=" N GLU G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU G 320 " --> pdb=" O TYR G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 344 Processing helix chain 'F' and resid 105 through 123 removed outlier: 3.900A pdb=" N LYS F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 137 removed outlier: 4.051A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 183 removed outlier: 3.799A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 200 removed outlier: 3.794A pdb=" N ILE F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 269 removed outlier: 3.572A pdb=" N GLY F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 311 removed outlier: 3.600A pdb=" N ILE F 309 " --> pdb=" O ASP F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 320 Processing helix chain 'F' and resid 329 through 342 Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.703A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA E 49 " --> pdb=" O ALA E 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 49' Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.651A pdb=" N ALA E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 123 removed outlier: 4.429A pdb=" N GLN E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 170 through 175 Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.611A pdb=" N PHE E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 200 removed outlier: 3.899A pdb=" N ALA E 197 " --> pdb=" O MET E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 303 Processing helix chain 'E' and resid 305 through 311 removed outlier: 3.748A pdb=" N SER E 308 " --> pdb=" O ASP E 305 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU E 310 " --> pdb=" O PHE E 307 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLN E 311 " --> pdb=" O SER E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 320 removed outlier: 3.813A pdb=" N TYR E 316 " --> pdb=" O GLN E 312 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 342 removed outlier: 3.761A pdb=" N ILE E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN E 332 " --> pdb=" O GLN E 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 removed outlier: 3.922A pdb=" N LEU D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA D 49 " --> pdb=" O ALA D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 49' Processing helix chain 'D' and resid 106 through 123 removed outlier: 3.875A pdb=" N GLN D 110 " --> pdb=" O SER D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 137 removed outlier: 4.181A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.522A pdb=" N ASN D 183 " --> pdb=" O GLN D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 199 Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 305 through 311 removed outlier: 3.517A pdb=" N ILE D 309 " --> pdb=" O ASP D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 320 Processing helix chain 'D' and resid 333 through 344 removed outlier: 3.698A pdb=" N GLY D 344 " --> pdb=" O ASN D 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.870A pdb=" N LYS C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 4.348A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 4.059A pdb=" N LEU C 142 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.796A pdb=" N PHE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 299 through 303 removed outlier: 3.600A pdb=" N GLY C 303 " --> pdb=" O PRO C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.539A pdb=" N ILE C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.774A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 removed outlier: 4.006A pdb=" N THR B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 removed outlier: 4.093A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 removed outlier: 3.788A pdb=" N TYR B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.634A pdb=" N ASN B 183 " --> pdb=" O GLN B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 200 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 312 through 320 Processing helix chain 'B' and resid 330 through 343 removed outlier: 4.103A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 10 removed outlier: 3.883A pdb=" N SER H 10 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 24 removed outlier: 4.162A pdb=" N LYS H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 44 removed outlier: 3.589A pdb=" N THR H 41 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE H 42 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 47 No H-bonds generated for 'chain 'H' and resid 45 through 47' Processing helix chain 'H' and resid 62 through 66 removed outlier: 4.439A pdb=" N LYS H 65 " --> pdb=" O CYS H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 80 removed outlier: 3.782A pdb=" N VAL H 79 " --> pdb=" O ILE H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 133 removed outlier: 3.635A pdb=" N SER H 133 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 153 removed outlier: 4.227A pdb=" N LEU H 152 " --> pdb=" O CYS H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 166 Processing helix chain 'H' and resid 174 through 182 removed outlier: 3.969A pdb=" N ALA H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 228 removed outlier: 4.244A pdb=" N ARG H 228 " --> pdb=" O HIS H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 231 No H-bonds generated for 'chain 'H' and resid 229 through 231' Processing helix chain 'H' and resid 232 through 236 Processing helix chain 'H' and resid 248 through 254 removed outlier: 4.148A pdb=" N CYS H 254 " --> pdb=" O THR H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 427 removed outlier: 4.115A pdb=" N PHE H 415 " --> pdb=" O SER H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 500 removed outlier: 3.538A pdb=" N LEU H 500 " --> pdb=" O VAL H 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 519 removed outlier: 3.903A pdb=" N HIS H 518 " --> pdb=" O ASP H 515 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE H 519 " --> pdb=" O PHE H 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 515 through 519' Processing helix chain 'H' and resid 528 through 532 removed outlier: 3.603A pdb=" N SER H 531 " --> pdb=" O ALA H 528 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU H 532 " --> pdb=" O ILE H 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 528 through 532' Processing helix chain 'H' and resid 550 through 555 Processing helix chain 'A' and resid 17 through 31 removed outlier: 4.060A pdb=" N LYS A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'J' and resid 14 through 26 Processing helix chain 'J' and resid 30 through 43 Processing helix chain 'J' and resid 67 through 82 removed outlier: 3.906A pdb=" N THR J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 134 Processing helix chain 'J' and resid 139 through 144 removed outlier: 3.896A pdb=" N TRP J 142 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS J 143 " --> pdb=" O TYR J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 204 Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.954A pdb=" N ARG J 220 " --> pdb=" O PRO J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 243 removed outlier: 3.597A pdb=" N PHE J 240 " --> pdb=" O ASP J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 265 Processing helix chain 'J' and resid 274 through 280 removed outlier: 3.563A pdb=" N LEU J 278 " --> pdb=" O ARG J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 309 removed outlier: 3.669A pdb=" N GLY J 301 " --> pdb=" O ASN J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 317 Processing helix chain 'J' and resid 327 through 332 Processing helix chain 'J' and resid 335 through 344 Processing helix chain 'J' and resid 369 through 379 Processing helix chain 'I' and resid 13 through 24 removed outlier: 3.717A pdb=" N PHE I 17 " --> pdb=" O SER I 13 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE I 18 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 4.165A pdb=" N PHE I 33 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 59 removed outlier: 3.714A pdb=" N ARG I 58 " --> pdb=" O ASP I 55 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE I 59 " --> pdb=" O ILE I 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 55 through 59' Processing helix chain 'I' and resid 60 through 64 removed outlier: 3.689A pdb=" N ALA I 64 " --> pdb=" O PRO I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 79 Processing helix chain 'I' and resid 128 through 135 removed outlier: 3.619A pdb=" N LEU I 132 " --> pdb=" O CYS I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 144 removed outlier: 4.275A pdb=" N HIS I 143 " --> pdb=" O TYR I 140 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE I 144 " --> pdb=" O LEU I 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 140 through 144' Processing helix chain 'I' and resid 196 through 202 Processing helix chain 'I' and resid 219 through 232 removed outlier: 3.541A pdb=" N LYS I 231 " --> pdb=" O TRP I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 244 Processing helix chain 'I' and resid 251 through 265 removed outlier: 4.173A pdb=" N LEU I 263 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS I 265 " --> pdb=" O PHE I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 285 removed outlier: 3.523A pdb=" N GLY I 285 " --> pdb=" O ARG I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 removed outlier: 3.783A pdb=" N LEU I 303 " --> pdb=" O ILE I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 332 Processing helix chain 'I' and resid 335 through 344 Processing helix chain 'I' and resid 368 through 375 Processing helix chain 'I' and resid 375 through 380 removed outlier: 3.579A pdb=" N PHE I 380 " --> pdb=" O TRP I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 386 through 390 removed outlier: 3.876A pdb=" N PHE I 389 " --> pdb=" O ASN I 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 7 through 8 removed outlier: 3.541A pdb=" N LYS G 102 " --> pdb=" O ALA G 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 29 through 31 removed outlier: 3.871A pdb=" N HIS G 84 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS G 151 " --> pdb=" O HIS G 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 35 through 41 Processing sheet with id=AA4, first strand: chain 'G' and resid 248 through 251 Processing sheet with id=AA5, first strand: chain 'F' and resid 7 through 8 Processing sheet with id=AA6, first strand: chain 'F' and resid 29 through 31 removed outlier: 3.704A pdb=" N HIS F 84 " --> pdb=" O VAL F 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 35 through 41 Processing sheet with id=AA8, first strand: chain 'F' and resid 248 through 249 removed outlier: 3.699A pdb=" N SER F 256 " --> pdb=" O THR F 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AB1, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.559A pdb=" N LYS E 102 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY E 345 " --> pdb=" O TYR E 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 13 through 15 Processing sheet with id=AB3, first strand: chain 'E' and resid 13 through 15 removed outlier: 3.931A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 35 through 42 Processing sheet with id=AB5, first strand: chain 'E' and resid 289 through 290 removed outlier: 3.909A pdb=" N THR E 295 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.606A pdb=" N HIS D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.686A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 35 through 42 Processing sheet with id=AB9, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AC1, first strand: chain 'C' and resid 102 through 103 removed outlier: 3.627A pdb=" N LYS C 102 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY C 345 " --> pdb=" O TYR C 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.501A pdb=" N CYS C 87 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 35 through 40 removed outlier: 3.721A pdb=" N ASN C 35 " --> pdb=" O PHE C 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AC5, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.747A pdb=" N HIS B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 72 through 75 removed outlier: 7.420A pdb=" N ILE A 146 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N THR B 38 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AC8, first strand: chain 'H' and resid 82 through 83 removed outlier: 3.565A pdb=" N SER H 122 " --> pdb=" O GLN H 83 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 203 through 204 Processing sheet with id=AD1, first strand: chain 'H' and resid 438 through 449 removed outlier: 6.373A pdb=" N PHE H 438 " --> pdb=" O ASN H 484 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN H 484 " --> pdb=" O PHE H 438 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE H 440 " --> pdb=" O ILE H 482 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE H 482 " --> pdb=" O ILE H 440 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL H 442 " --> pdb=" O SER H 480 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER H 480 " --> pdb=" O VAL H 442 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS H 446 " --> pdb=" O ASP H 476 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N CYS H 475 " --> pdb=" O CYS H 396 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N CYS H 396 " --> pdb=" O CYS H 475 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL H 477 " --> pdb=" O ARG H 394 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG H 394 " --> pdb=" O VAL H 477 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE H 479 " --> pdb=" O ASN H 392 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN H 392 " --> pdb=" O PHE H 479 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU H 504 " --> pdb=" O GLY H 507 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 438 through 449 removed outlier: 6.373A pdb=" N PHE H 438 " --> pdb=" O ASN H 484 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN H 484 " --> pdb=" O PHE H 438 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE H 440 " --> pdb=" O ILE H 482 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE H 482 " --> pdb=" O ILE H 440 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL H 442 " --> pdb=" O SER H 480 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER H 480 " --> pdb=" O VAL H 442 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS H 446 " --> pdb=" O ASP H 476 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N CYS H 475 " --> pdb=" O CYS H 396 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N CYS H 396 " --> pdb=" O CYS H 475 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL H 477 " --> pdb=" O ARG H 394 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG H 394 " --> pdb=" O VAL H 477 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE H 479 " --> pdb=" O ASN H 392 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN H 392 " --> pdb=" O PHE H 479 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN H 520 " --> pdb=" O VAL H 389 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 539 through 542 removed outlier: 3.592A pdb=" N TRP H 539 " --> pdb=" O ILE H 601 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 591 through 594 removed outlier: 4.014A pdb=" N GLY H 569 " --> pdb=" O ILE H 594 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AD6, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.804A pdb=" N HIS A 150 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 107 through 110 Processing sheet with id=AD8, first strand: chain 'J' and resid 322 through 323 removed outlier: 3.573A pdb=" N MET J 323 " --> pdb=" O PHE J 367 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE J 367 " --> pdb=" O MET J 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'I' and resid 94 through 100 removed outlier: 4.290A pdb=" N THR I 97 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ALA I 107 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 149 through 150 814 hydrogen bonds defined for protein. 2283 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 5.40 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7859 1.33 - 1.45: 6773 1.45 - 1.58: 14838 1.58 - 1.70: 118 1.70 - 1.82: 216 Bond restraints: 29804 Sorted by residual: bond pdb=" CB VAL D 23 " pdb=" CG2 VAL D 23 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.19e+00 bond pdb=" CG1 ILE G 171 " pdb=" CD1 ILE G 171 " ideal model delta sigma weight residual 1.513 1.410 0.103 3.90e-02 6.57e+02 6.99e+00 bond pdb=" C LYS H 579 " pdb=" N PRO H 580 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.72e+00 bond pdb=" CB VAL F 23 " pdb=" CG2 VAL F 23 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.87e+00 bond pdb=" CG1 ILE B 13 " pdb=" CD1 ILE B 13 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.72e+00 ... (remaining 29799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 39684 3.14 - 6.28: 899 6.28 - 9.42: 123 9.42 - 12.57: 23 12.57 - 15.71: 8 Bond angle restraints: 40737 Sorted by residual: angle pdb=" C PHE A 193 " pdb=" N GLN A 194 " pdb=" CA GLN A 194 " ideal model delta sigma weight residual 120.94 134.27 -13.33 1.90e+00 2.77e-01 4.92e+01 angle pdb=" N VAL H 79 " pdb=" CA VAL H 79 " pdb=" C VAL H 79 " ideal model delta sigma weight residual 112.96 106.02 6.94 1.00e+00 1.00e+00 4.81e+01 angle pdb=" CA TRP J 203 " pdb=" CB TRP J 203 " pdb=" CG TRP J 203 " ideal model delta sigma weight residual 113.60 126.06 -12.46 1.90e+00 2.77e-01 4.30e+01 angle pdb=" O3' G M 15 " pdb=" C3' G M 15 " pdb=" C2' G M 15 " ideal model delta sigma weight residual 109.50 101.27 8.23 1.50e+00 4.44e-01 3.01e+01 angle pdb=" C LYS I 276 " pdb=" N ASP I 277 " pdb=" CA ASP I 277 " ideal model delta sigma weight residual 123.47 131.66 -8.19 1.53e+00 4.27e-01 2.87e+01 ... (remaining 40732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 17297 34.29 - 68.59: 246 68.59 - 102.88: 18 102.88 - 137.17: 1 137.17 - 171.46: 5 Dihedral angle restraints: 17567 sinusoidal: 7465 harmonic: 10102 Sorted by residual: dihedral pdb=" CA VAL D 52 " pdb=" C VAL D 52 " pdb=" N SER D 53 " pdb=" CA SER D 53 " ideal model delta harmonic sigma weight residual -180.00 -116.38 -63.62 0 5.00e+00 4.00e-02 1.62e+02 dihedral pdb=" CA SER H 242 " pdb=" C SER H 242 " pdb=" N ARG H 243 " pdb=" CA ARG H 243 " ideal model delta harmonic sigma weight residual 180.00 135.12 44.88 0 5.00e+00 4.00e-02 8.06e+01 dihedral pdb=" O4' C M 38 " pdb=" C1' C M 38 " pdb=" N1 C M 38 " pdb=" C2 C M 38 " ideal model delta sinusoidal sigma weight residual 232.00 60.54 171.46 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 17564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3671 0.083 - 0.167: 727 0.167 - 0.250: 79 0.250 - 0.334: 18 0.334 - 0.417: 3 Chirality restraints: 4498 Sorted by residual: chirality pdb=" CB ILE J 94 " pdb=" CA ILE J 94 " pdb=" CG1 ILE J 94 " pdb=" CG2 ILE J 94 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" C3' U M 2 " pdb=" C4' U M 2 " pdb=" O3' U M 2 " pdb=" C2' U M 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA SER D 53 " pdb=" N SER D 53 " pdb=" C SER D 53 " pdb=" CB SER D 53 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 4495 not shown) Planarity restraints: 4998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 203 " 0.047 2.00e-02 2.50e+03 3.16e-02 2.50e+01 pdb=" CG TRP J 203 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP J 203 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP J 203 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 203 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP J 203 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 203 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 203 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 203 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 203 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 181 " 0.040 2.00e-02 2.50e+03 2.59e-02 1.17e+01 pdb=" CG PHE A 181 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 181 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 181 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 181 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 181 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE A 181 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 9 " 0.022 2.00e-02 2.50e+03 2.40e-02 1.15e+01 pdb=" CG TYR E 9 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR E 9 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR E 9 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR E 9 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR E 9 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 9 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 9 " 0.002 2.00e-02 2.50e+03 ... (remaining 4995 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 3 2.22 - 2.89: 10681 2.89 - 3.56: 36734 3.56 - 4.23: 64729 4.23 - 4.90: 110587 Nonbonded interactions: 222734 Sorted by model distance: nonbonded pdb=" O2' A M 7 " pdb=" O THR H 453 " model vdw 1.550 3.040 nonbonded pdb=" N7 G M 41 " pdb=" NH2 ARG B 244 " model vdw 2.033 3.200 nonbonded pdb=" OP1 C M 29 " pdb=" NH2 ARG D 222 " model vdw 2.100 3.120 nonbonded pdb=" OG SER C 12 " pdb=" O SER C 94 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A 19 " pdb=" O VAL I 268 " model vdw 2.254 3.040 ... (remaining 222729 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 'B' and (resid 2 through 322 or resid 325 through 349)) selection = (chain 'C' and (resid 2 through 43 or resid 70 through 229 or resid 243 through \ 322 or resid 325 through 349)) selection = (chain 'D' and (resid 2 through 43 or resid 70 through 229 or resid 243 through \ 322 or resid 325 through 349)) selection = (chain 'E' and (resid 2 through 43 or resid 70 through 229 or resid 243 through \ 322 or resid 325 through 349)) selection = (chain 'F' and (resid 2 through 43 or resid 70 through 229 or resid 243 through \ 349)) selection = (chain 'G' and (resid 2 through 43 or resid 70 through 229 or resid 243 through \ 322 or resid 325 through 349)) } ncs_group { reference = chain 'I' selection = chain 'J' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 27.350 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 : 0.009 0.103 29804 Z= 0.366 Angle : 1.168 15.706 40737 Z= 0.650 Chirality : 0.068 0.417 4498 Planarity : 0.009 0.080 4998 Dihedral : 13.124 171.465 11005 Min Nonbonded Distance : 1.550 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 0.20 % Allowed : 4.43 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.31 % 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: -4.69 (0.11), residues: 3395 helix: -3.57 (0.10), residues: 955 sheet: -1.39 (0.23), residues: 500 loop : -3.49 (0.11), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG E 283 TYR 0.057 0.004 TYR E 9 PHE 0.055 0.004 PHE C 89 TRP 0.085 0.004 TRP J 203 HIS 0.019 0.003 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00867 / 0.37 (29804) covalent geometry : angle 1.16758 / 0.65 (40737) hydrogen bonds : bond 0.17354 / 10.20 ( 816) hydrogen bonds : angle 7.06190 / 4.19 ( 2305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 336 time to evaluate : 1.039 Fit side-chains REVERT: G 14 ASP cc_start: 0.7940 (p0) cc_final: 0.7714 (p0) REVERT: F 334 MET cc_start: 0.7314 (ptp) cc_final: 0.7072 (ptp) REVERT: D 96 GLU cc_start: 0.7943 (mp0) cc_final: 0.7710 (mp0) REVERT: C 155 VAL cc_start: 0.8760 (m) cc_final: 0.8523 (p) REVERT: C 192 GLU cc_start: 0.7973 (tp30) cc_final: 0.7695 (tp30) REVERT: B 43 MET cc_start: 0.4152 (mpt) cc_final: 0.3881 (mpt) REVERT: B 107 LYS cc_start: 0.7794 (mppt) cc_final: 0.7575 (mmmt) REVERT: H 126 ASP cc_start: 0.5732 (t70) cc_final: 0.5348 (t0) REVERT: H 258 PHE cc_start: 0.6957 (m-80) cc_final: 0.6721 (m-80) REVERT: H 434 ARG cc_start: 0.5658 (mmt90) cc_final: 0.4538 (mmm160) REVERT: A 184 TYR cc_start: 0.5421 (p90) cc_final: 0.4951 (p90) REVERT: J 99 MET cc_start: 0.4170 (mtp) cc_final: 0.3372 (ttp) REVERT: J 141 LEU cc_start: 0.7030 (tp) cc_final: 0.6666 (tp) REVERT: J 228 MET cc_start: 0.3564 (mtp) cc_final: 0.3270 (mtp) outliers start: 6 outliers final: 1 residues processed: 342 average time/residue: 0.1835 time to fit residues: 100.5425 Evaluate side-chains 236 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 179 GLN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS F 145 ASN F 214 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN E 153 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN D 290 HIS ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B 183 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN H 77 ASN H 80 ASN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 HIS H 131 ASN H 162 ASN H 420 HIS ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 518 HIS H 548 ASN ** H 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 ASN A 39 ASN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN J 42 GLN J 50 GLN J 98 ASN J 151 HIS J 214 ASN J 324 ASN J 381 GLN I 23 ASN I 320 ASN ** I 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.227709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.202180 restraints weight = 35326.799| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.25 r_work: 0.3838 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 29804 Z= 0.121 Angle : 0.627 9.487 40737 Z= 0.334 Chirality : 0.044 0.213 4498 Planarity : 0.006 0.061 4998 Dihedral : 11.257 179.065 4433 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.41 % Allowed : 6.90 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.12), residues: 3395 helix: -2.20 (0.14), residues: 987 sheet: -1.01 (0.23), residues: 503 loop : -3.00 (0.12), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 240 TYR 0.020 0.001 TYR J 219 PHE 0.025 0.001 PHE J 240 TRP 0.042 0.002 TRP J 203 HIS 0.010 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (29804) covalent geometry : angle 0.62742 / 0.33 (40737) hydrogen bonds : bond 0.04152 / 2.50 ( 816) hydrogen bonds : angle 5.35657 / 3.24 ( 2305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 305 time to evaluate : 0.879 Fit side-chains REVERT: G 181 PHE cc_start: 0.7837 (m-80) cc_final: 0.7585 (m-80) REVERT: G 297 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.6410 (p90) REVERT: E 107 LYS cc_start: 0.7868 (tmtt) cc_final: 0.7653 (tmtt) REVERT: E 122 LYS cc_start: 0.7837 (tppp) cc_final: 0.7619 (tptt) REVERT: E 202 ASP cc_start: 0.7027 (p0) cc_final: 0.6753 (p0) REVERT: D 347 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7352 (p90) REVERT: C 122 LYS cc_start: 0.7771 (tptt) cc_final: 0.7461 (tptt) REVERT: B 107 LYS cc_start: 0.8079 (mppt) cc_final: 0.7835 (mmmt) REVERT: H 125 HIS cc_start: 0.6790 (t-90) cc_final: 0.6521 (t-170) REVERT: H 126 ASP cc_start: 0.6317 (t70) cc_final: 0.5927 (t0) REVERT: H 434 ARG cc_start: 0.5514 (mmt90) cc_final: 0.4722 (mmm160) REVERT: H 557 MET cc_start: 0.5998 (ttp) cc_final: 0.5676 (ttm) REVERT: H 564 MET cc_start: 0.6687 (mmm) cc_final: 0.6300 (mmm) REVERT: A 169 MET cc_start: 0.6349 (tmt) cc_final: 0.5862 (tmm) REVERT: J 215 LEU cc_start: -0.1949 (OUTLIER) cc_final: -0.2223 (pp) outliers start: 43 outliers final: 17 residues processed: 337 average time/residue: 0.1834 time to fit residues: 98.6473 Evaluate side-chains 256 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 534 ILE Chi-restraints excluded: chain H residue 625 VAL Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 373 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 220 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 chunk 232 optimal weight: 3.9990 chunk 218 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 281 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 184 ASN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS F 135 ASN E 69 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 HIS ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 581 ASN A 32 ASN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 252 HIS I 320 ASN ** I 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.226817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.169255 restraints weight = 35271.240| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 6.93 r_work: 0.3180 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29804 Z= 0.135 Angle : 0.604 9.605 40737 Z= 0.318 Chirality : 0.043 0.251 4498 Planarity : 0.005 0.058 4998 Dihedral : 10.493 177.213 4432 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.14 % Allowed : 8.77 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.13), residues: 3395 helix: -1.57 (0.15), residues: 994 sheet: -0.83 (0.23), residues: 503 loop : -2.78 (0.12), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 222 TYR 0.020 0.002 TYR J 219 PHE 0.024 0.001 PHE J 240 TRP 0.034 0.002 TRP J 203 HIS 0.007 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (29804) covalent geometry : angle 0.60448 / 0.32 (40737) hydrogen bonds : bond 0.04175 / 2.51 ( 816) hydrogen bonds : angle 5.00386 / 3.02 ( 2305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 255 time to evaluate : 0.820 Fit side-chains REVERT: G 181 PHE cc_start: 0.8081 (m-80) cc_final: 0.7753 (m-80) REVERT: G 297 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.6000 (p90) REVERT: E 96 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: E 107 LYS cc_start: 0.8157 (tmtt) cc_final: 0.7945 (tmtt) REVERT: D 202 ASP cc_start: 0.7796 (p0) cc_final: 0.7554 (p0) REVERT: D 252 ASP cc_start: 0.8090 (m-30) cc_final: 0.7873 (m-30) REVERT: D 284 VAL cc_start: 0.9312 (OUTLIER) cc_final: 0.9107 (m) REVERT: D 347 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7661 (p90) REVERT: C 122 LYS cc_start: 0.7787 (tptt) cc_final: 0.7485 (tptp) REVERT: B 316 TYR cc_start: 0.8255 (m-80) cc_final: 0.7931 (m-80) REVERT: H 434 ARG cc_start: 0.5099 (mmt90) cc_final: 0.3986 (mmm160) REVERT: H 493 GLN cc_start: 0.6300 (mm110) cc_final: 0.3745 (tt0) REVERT: A 169 MET cc_start: 0.5076 (tmt) cc_final: 0.4548 (tmm) REVERT: J 228 MET cc_start: 0.3687 (mtp) cc_final: 0.3416 (mtp) REVERT: I 342 MET cc_start: 0.4935 (OUTLIER) cc_final: 0.4261 (ttt) outliers start: 65 outliers final: 33 residues processed: 298 average time/residue: 0.1733 time to fit residues: 83.5579 Evaluate side-chains 273 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 534 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain I residue 342 MET Chi-restraints excluded: chain I residue 373 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 199 optimal weight: 8.9990 chunk 308 optimal weight: 50.0000 chunk 60 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 141 optimal weight: 0.0970 chunk 179 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 581 ASN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 ASN ** I 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.228434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.203162 restraints weight = 35155.110| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 1.27 r_work: 0.3875 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29804 Z= 0.104 Angle : 0.550 9.241 40737 Z= 0.288 Chirality : 0.042 0.324 4498 Planarity : 0.005 0.054 4998 Dihedral : 10.211 178.475 4432 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.33 % Allowed : 9.89 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.13), residues: 3395 helix: -1.08 (0.16), residues: 987 sheet: -0.66 (0.23), residues: 509 loop : -2.59 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 11 TYR 0.016 0.001 TYR C 275 PHE 0.022 0.001 PHE J 240 TRP 0.024 0.001 TRP J 203 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (29804) covalent geometry : angle 0.55013 / 0.29 (40737) hydrogen bonds : bond 0.03498 / 2.12 ( 816) hydrogen bonds : angle 4.75675 / 2.88 ( 2305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 264 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: G 297 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.6011 (p90) REVERT: G 315 HIS cc_start: 0.7993 (t-90) cc_final: 0.7537 (t-170) REVERT: E 107 LYS cc_start: 0.7904 (tmtt) cc_final: 0.7703 (tmtt) REVERT: E 122 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7394 (tttp) REVERT: D 202 ASP cc_start: 0.7728 (p0) cc_final: 0.7393 (p0) REVERT: D 347 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7437 (p90) REVERT: H 493 GLN cc_start: 0.6480 (mm110) cc_final: 0.4315 (tt0) REVERT: H 530 GLU cc_start: 0.5543 (pm20) cc_final: 0.4107 (pm20) REVERT: H 557 MET cc_start: 0.6235 (ttp) cc_final: 0.6021 (ptm) REVERT: A 14 LEU cc_start: 0.4926 (OUTLIER) cc_final: 0.4686 (tm) REVERT: A 169 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.6047 (tmm) REVERT: I 311 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6875 (mm) REVERT: I 342 MET cc_start: 0.5131 (OUTLIER) cc_final: 0.4833 (ttt) outliers start: 71 outliers final: 31 residues processed: 315 average time/residue: 0.1657 time to fit residues: 84.7124 Evaluate side-chains 274 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 534 ILE Chi-restraints excluded: chain H residue 561 HIS Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain I residue 342 MET Chi-restraints excluded: chain I residue 373 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 134 optimal weight: 4.9990 chunk 277 optimal weight: 0.7980 chunk 210 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 343 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 205 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 GLN E 162 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 GLN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 ASN I 338 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.219205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.171800 restraints weight = 35354.093| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.97 r_work: 0.3488 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29804 Z= 0.139 Angle : 0.586 9.449 40737 Z= 0.305 Chirality : 0.043 0.250 4498 Planarity : 0.005 0.053 4998 Dihedral : 10.039 177.943 4432 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.37 % Allowed : 11.24 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.14), residues: 3395 helix: -0.92 (0.16), residues: 989 sheet: -0.58 (0.24), residues: 506 loop : -2.52 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 283 TYR 0.013 0.001 TYR D 275 PHE 0.024 0.001 PHE J 240 TRP 0.022 0.001 TRP J 203 HIS 0.006 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (29804) covalent geometry : angle 0.58627 / 0.31 (40737) hydrogen bonds : bond 0.03887 / 2.33 ( 816) hydrogen bonds : angle 4.73725 / 2.85 ( 2305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 237 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: G 297 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.6167 (p90) REVERT: E 74 ASP cc_start: 0.8827 (m-30) cc_final: 0.8558 (m-30) REVERT: E 122 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7279 (tttt) REVERT: D 123 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7086 (mp) REVERT: D 202 ASP cc_start: 0.7855 (p0) cc_final: 0.7361 (p0) REVERT: D 347 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7505 (p90) REVERT: B 107 LYS cc_start: 0.8227 (mppt) cc_final: 0.7975 (mmmt) REVERT: H 434 ARG cc_start: 0.5560 (mmt90) cc_final: 0.4555 (mmm160) REVERT: H 530 GLU cc_start: 0.5597 (pm20) cc_final: 0.4236 (pm20) REVERT: H 557 MET cc_start: 0.6101 (ttp) cc_final: 0.5808 (ptm) REVERT: H 562 GLN cc_start: 0.4800 (OUTLIER) cc_final: 0.3895 (tm130) REVERT: A 14 LEU cc_start: 0.4746 (OUTLIER) cc_final: 0.4531 (tm) REVERT: A 169 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.5510 (tmm) REVERT: J 94 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.6519 (tt) REVERT: I 311 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6418 (mm) REVERT: I 333 ASN cc_start: 0.6666 (OUTLIER) cc_final: 0.6422 (m-40) REVERT: I 345 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.6656 (tt0) outliers start: 72 outliers final: 48 residues processed: 288 average time/residue: 0.1672 time to fit residues: 78.3587 Evaluate side-chains 285 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 226 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 448 GLU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 534 ILE Chi-restraints excluded: chain H residue 561 HIS Chi-restraints excluded: chain H residue 562 GLN Chi-restraints excluded: chain H residue 579 LYS Chi-restraints excluded: chain H residue 625 VAL Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain I residue 345 GLN Chi-restraints excluded: chain I residue 373 PHE Chi-restraints excluded: chain I residue 377 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 220 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 322 optimal weight: 0.0370 chunk 219 optimal weight: 2.9990 chunk 326 optimal weight: 20.0000 chunk 318 optimal weight: 10.0000 chunk 310 optimal weight: 30.0000 chunk 294 optimal weight: 50.0000 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS F 312 GLN E 162 ASN D 214 HIS ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 GLN H 571 HIS ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 HIS J 237 HIS I 320 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.215333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.169534 restraints weight = 34790.622| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.63 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 29804 Z= 0.243 Angle : 0.705 9.874 40737 Z= 0.365 Chirality : 0.048 0.316 4498 Planarity : 0.006 0.057 4998 Dihedral : 10.374 178.193 4432 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 3.02 % Allowed : 11.47 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.13), residues: 3395 helix: -1.09 (0.16), residues: 989 sheet: -0.68 (0.24), residues: 509 loop : -2.61 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 283 TYR 0.021 0.002 TYR H 622 PHE 0.032 0.002 PHE C 89 TRP 0.026 0.002 TRP J 203 HIS 0.008 0.002 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.24 (29804) covalent geometry : angle 0.70512 / 0.36 (40737) hydrogen bonds : bond 0.05120 / 3.03 ( 816) hydrogen bonds : angle 4.96994 / 2.97 ( 2305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 239 time to evaluate : 0.717 Fit side-chains REVERT: G 169 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: G 297 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6735 (p90) REVERT: F 97 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8149 (pt) REVERT: D 97 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8646 (pt) REVERT: D 277 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.5056 (pp20) REVERT: D 347 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7850 (p90) REVERT: C 155 VAL cc_start: 0.8753 (m) cc_final: 0.8519 (p) REVERT: H 434 ARG cc_start: 0.6126 (mmt90) cc_final: 0.5437 (mmm160) REVERT: H 530 GLU cc_start: 0.5456 (pm20) cc_final: 0.4072 (pm20) REVERT: H 564 MET cc_start: 0.6505 (mmm) cc_final: 0.6121 (mmm) REVERT: A 14 LEU cc_start: 0.4842 (OUTLIER) cc_final: 0.4638 (tm) REVERT: A 169 MET cc_start: 0.5887 (OUTLIER) cc_final: 0.5381 (tmm) REVERT: J 78 LEU cc_start: 0.7504 (mp) cc_final: 0.7077 (mp) REVERT: J 94 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7256 (tt) REVERT: J 228 MET cc_start: 0.2601 (mtp) cc_final: 0.2271 (mpp) REVERT: J 291 GLU cc_start: 0.5042 (OUTLIER) cc_final: 0.4842 (tm-30) REVERT: I 311 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6568 (mm) REVERT: I 345 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.6335 (tt0) outliers start: 92 outliers final: 57 residues processed: 305 average time/residue: 0.1605 time to fit residues: 80.4325 Evaluate side-chains 293 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 224 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 448 GLU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 494 ASP Chi-restraints excluded: chain H residue 513 ILE Chi-restraints excluded: chain H residue 534 ILE Chi-restraints excluded: chain H residue 561 HIS Chi-restraints excluded: chain H residue 625 VAL Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 291 GLU Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain I residue 345 GLN Chi-restraints excluded: chain I residue 373 PHE Chi-restraints excluded: chain I residue 377 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 133 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 303 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 226 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 266 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 270 optimal weight: 30.0000 chunk 31 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 349 HIS H 64 GLN ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 GLN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.220915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.162874 restraints weight = 34930.939| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 7.27 r_work: 0.3215 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29804 Z= 0.107 Angle : 0.556 9.042 40737 Z= 0.290 Chirality : 0.042 0.254 4498 Planarity : 0.005 0.076 4998 Dihedral : 9.898 178.829 4432 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.73 % Allowed : 11.47 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.14), residues: 3395 helix: -0.76 (0.17), residues: 998 sheet: -0.45 (0.24), residues: 509 loop : -2.43 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 538 TYR 0.017 0.001 TYR C 275 PHE 0.024 0.001 PHE J 240 TRP 0.023 0.001 TRP J 203 HIS 0.006 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (29804) covalent geometry : angle 0.55578 / 0.29 (40737) hydrogen bonds : bond 0.03404 / 2.05 ( 816) hydrogen bonds : angle 4.66576 / 2.81 ( 2305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 244 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: G 27 ASP cc_start: 0.7570 (m-30) cc_final: 0.7363 (m-30) REVERT: G 297 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.5962 (p90) REVERT: F 97 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8363 (pt) REVERT: E 74 ASP cc_start: 0.8994 (m-30) cc_final: 0.8632 (m-30) REVERT: E 122 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7337 (tttp) REVERT: D 97 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8656 (pt) REVERT: D 314 GLU cc_start: 0.8053 (mp0) cc_final: 0.7129 (mm-30) REVERT: D 330 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.8027 (m) REVERT: D 347 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7636 (p90) REVERT: C 171 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8915 (mp) REVERT: H 434 ARG cc_start: 0.4801 (mmt90) cc_final: 0.3754 (mmm160) REVERT: H 496 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6559 (tm) REVERT: H 530 GLU cc_start: 0.5242 (pm20) cc_final: 0.4212 (pm20) REVERT: H 557 MET cc_start: 0.5640 (ttp) cc_final: 0.5205 (ptm) REVERT: H 562 GLN cc_start: 0.3771 (OUTLIER) cc_final: 0.3272 (tm130) REVERT: A 169 MET cc_start: 0.4995 (OUTLIER) cc_final: 0.4429 (tmm) REVERT: J 291 GLU cc_start: 0.5304 (OUTLIER) cc_final: 0.4946 (tm-30) REVERT: I 311 LEU cc_start: 0.5617 (OUTLIER) cc_final: 0.5014 (mm) REVERT: I 333 ASN cc_start: 0.6053 (OUTLIER) cc_final: 0.5635 (m-40) outliers start: 83 outliers final: 50 residues processed: 304 average time/residue: 0.1619 time to fit residues: 79.2773 Evaluate side-chains 295 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 232 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 448 GLU Chi-restraints excluded: chain H residue 496 LEU Chi-restraints excluded: chain H residue 513 ILE Chi-restraints excluded: chain H residue 534 ILE Chi-restraints excluded: chain H residue 562 GLN Chi-restraints excluded: chain H residue 579 LYS Chi-restraints excluded: chain H residue 625 VAL Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 291 GLU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain I residue 373 PHE Chi-restraints excluded: chain I residue 377 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 156 optimal weight: 0.9980 chunk 310 optimal weight: 10.0000 chunk 330 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 289 optimal weight: 9.9990 chunk 326 optimal weight: 5.9990 chunk 214 optimal weight: 0.0670 chunk 296 optimal weight: 40.0000 chunk 50 optimal weight: 2.9990 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 ASN G 114 GLN F 183 ASN E 162 ASN C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN H 562 GLN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.215590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.169206 restraints weight = 34872.426| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.72 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 29804 Z= 0.241 Angle : 0.700 9.397 40737 Z= 0.361 Chirality : 0.049 0.752 4498 Planarity : 0.006 0.071 4998 Dihedral : 10.112 176.540 4432 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.02 % Allowed : 11.60 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.13), residues: 3395 helix: -0.96 (0.16), residues: 995 sheet: -0.63 (0.24), residues: 509 loop : -2.56 (0.13), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 283 TYR 0.017 0.002 TYR F 275 PHE 0.037 0.002 PHE I 367 TRP 0.022 0.002 TRP J 203 HIS 0.010 0.002 HIS H 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.24 (29804) covalent geometry : angle 0.69975 / 0.36 (40737) hydrogen bonds : bond 0.04935 / 2.92 ( 816) hydrogen bonds : angle 4.87929 / 2.91 ( 2305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 225 time to evaluate : 0.912 Fit side-chains REVERT: G 297 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6744 (p90) REVERT: F 97 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8177 (pt) REVERT: E 340 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.7729 (m-40) REVERT: D 97 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8675 (pt) REVERT: D 244 ARG cc_start: 0.8609 (ttt180) cc_final: 0.8369 (ttp-170) REVERT: D 277 GLU cc_start: 0.5006 (mp0) cc_final: 0.4683 (mp0) REVERT: D 330 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7657 (m) REVERT: D 347 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7909 (p90) REVERT: C 155 VAL cc_start: 0.8799 (m) cc_final: 0.8584 (p) REVERT: H 434 ARG cc_start: 0.6146 (mmt90) cc_final: 0.5400 (mmm160) REVERT: H 496 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7303 (tm) REVERT: H 530 GLU cc_start: 0.5514 (pm20) cc_final: 0.4131 (pm20) REVERT: H 557 MET cc_start: 0.6230 (ttp) cc_final: 0.5927 (ptm) REVERT: A 169 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.5667 (tmt) REVERT: J 228 MET cc_start: 0.2864 (mtp) cc_final: 0.2506 (mpp) REVERT: J 291 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.5213 (tm-30) REVERT: I 311 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6778 (mm) outliers start: 92 outliers final: 61 residues processed: 292 average time/residue: 0.1684 time to fit residues: 80.4440 Evaluate side-chains 289 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 218 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 448 GLU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 494 ASP Chi-restraints excluded: chain H residue 496 LEU Chi-restraints excluded: chain H residue 513 ILE Chi-restraints excluded: chain H residue 534 ILE Chi-restraints excluded: chain H residue 563 LEU Chi-restraints excluded: chain H residue 625 VAL Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain J residue 291 GLU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain I residue 373 PHE Chi-restraints excluded: chain I residue 377 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 37 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 46 optimal weight: 0.0370 chunk 215 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 283 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 207 optimal weight: 7.9990 chunk 266 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 ASN ** A 148 HIS ** 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 = 0.4334 r_free = 0.4334 target = 0.219209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.161483 restraints weight = 34768.168| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 6.83 r_work: 0.3203 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29804 Z= 0.126 Angle : 0.585 8.810 40737 Z= 0.304 Chirality : 0.043 0.600 4498 Planarity : 0.005 0.061 4998 Dihedral : 9.827 179.752 4432 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.69 % Allowed : 12.09 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.14), residues: 3395 helix: -0.72 (0.17), residues: 997 sheet: -0.47 (0.24), residues: 511 loop : -2.42 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 286 TYR 0.015 0.001 TYR J 219 PHE 0.024 0.001 PHE J 240 TRP 0.020 0.001 TRP J 203 HIS 0.007 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (29804) covalent geometry : angle 0.58546 / 0.30 (40737) hydrogen bonds : bond 0.03684 / 2.21 ( 816) hydrogen bonds : angle 4.67284 / 2.80 ( 2305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 234 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 27 ASP cc_start: 0.7619 (m-30) cc_final: 0.7401 (m-30) REVERT: G 297 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.6180 (p90) REVERT: F 97 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8407 (pt) REVERT: E 74 ASP cc_start: 0.9025 (m-30) cc_final: 0.8674 (m-30) REVERT: E 122 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7379 (tttp) REVERT: D 97 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8660 (pt) REVERT: D 277 GLU cc_start: 0.5416 (mp0) cc_final: 0.5044 (mp0) REVERT: D 330 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8029 (m) REVERT: H 211 ILE cc_start: 0.6691 (mm) cc_final: 0.6391 (mm) REVERT: H 259 ARG cc_start: 0.6640 (ptp-170) cc_final: 0.6352 (ptp-170) REVERT: H 434 ARG cc_start: 0.5049 (mmt90) cc_final: 0.3943 (mmm160) REVERT: H 496 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6749 (tm) REVERT: H 530 GLU cc_start: 0.5201 (pm20) cc_final: 0.4131 (pm20) REVERT: H 557 MET cc_start: 0.5797 (ttp) cc_final: 0.5275 (ptm) REVERT: H 563 LEU cc_start: 0.4562 (OUTLIER) cc_final: 0.3165 (tt) REVERT: A 169 MET cc_start: 0.4835 (OUTLIER) cc_final: 0.4513 (tmt) REVERT: J 228 MET cc_start: 0.3786 (mtp) cc_final: 0.3334 (mpp) REVERT: J 291 GLU cc_start: 0.5324 (OUTLIER) cc_final: 0.4965 (tm-30) REVERT: I 311 LEU cc_start: 0.5674 (OUTLIER) cc_final: 0.5112 (mm) outliers start: 82 outliers final: 59 residues processed: 291 average time/residue: 0.1669 time to fit residues: 77.8558 Evaluate side-chains 293 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 224 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 274 TRP Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 239 THR Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 448 GLU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 496 LEU Chi-restraints excluded: chain H residue 513 ILE Chi-restraints excluded: chain H residue 534 ILE Chi-restraints excluded: chain H residue 563 LEU Chi-restraints excluded: chain H residue 625 VAL Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain J residue 291 GLU Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain I residue 373 PHE Chi-restraints excluded: chain I residue 377 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7351 > 50: distance: 75 - 79: 30.033 distance: 79 - 80: 14.571 distance: 80 - 81: 26.137 distance: 80 - 83: 33.602 distance: 81 - 82: 47.418 distance: 81 - 87: 18.793 distance: 83 - 84: 8.671 distance: 84 - 85: 44.039 distance: 84 - 86: 45.759 distance: 87 - 88: 16.654 distance: 87 - 93: 37.614 distance: 88 - 89: 46.380 distance: 89 - 90: 41.487 distance: 89 - 94: 22.073 distance: 91 - 92: 41.260 distance: 92 - 93: 11.289 distance: 94 - 95: 30.856 distance: 95 - 96: 12.326 distance: 95 - 98: 32.499 distance: 96 - 97: 39.191 distance: 96 - 103: 38.850 distance: 98 - 99: 28.826 distance: 99 - 100: 50.345 distance: 100 - 101: 16.704 distance: 100 - 102: 31.846 distance: 103 - 104: 40.364 distance: 104 - 105: 16.358 distance: 104 - 107: 27.749 distance: 105 - 106: 50.470 distance: 105 - 114: 39.725 distance: 107 - 108: 50.839 distance: 108 - 109: 25.820 distance: 109 - 110: 5.499 distance: 110 - 111: 20.213 distance: 111 - 112: 26.793 distance: 111 - 113: 11.292 distance: 115 - 116: 39.893 distance: 115 - 118: 16.156 distance: 116 - 117: 35.238 distance: 116 - 122: 50.496 distance: 118 - 119: 15.725 distance: 119 - 120: 21.325 distance: 119 - 121: 23.432 distance: 122 - 123: 12.269 distance: 123 - 124: 41.984 distance: 123 - 126: 20.818 distance: 124 - 125: 32.496 distance: 124 - 130: 31.908 distance: 126 - 127: 31.518 distance: 127 - 128: 34.394 distance: 127 - 129: 35.952 distance: 130 - 131: 50.677 distance: 131 - 132: 35.136 distance: 131 - 134: 27.296 distance: 132 - 133: 52.670 distance: 132 - 139: 40.131 distance: 134 - 135: 29.078 distance: 135 - 136: 31.094 distance: 136 - 137: 45.588 distance: 136 - 138: 18.208 distance: 139 - 140: 25.265 distance: 140 - 141: 4.039 distance: 140 - 143: 11.814 distance: 141 - 142: 14.693 distance: 141 - 149: 18.567 distance: 143 - 144: 41.963 distance: 144 - 145: 11.013 distance: 144 - 146: 38.387 distance: 145 - 147: 26.103 distance: 146 - 148: 16.108 distance: 147 - 148: 29.979 distance: 149 - 150: 17.387 distance: 150 - 151: 32.192 distance: 150 - 153: 32.640 distance: 151 - 152: 25.070 distance: 151 - 157: 25.069 distance: 153 - 154: 24.869 distance: 154 - 155: 30.372 distance: 154 - 156: 30.268 distance: 157 - 158: 39.015 distance: 158 - 159: 21.178 distance: 158 - 161: 25.944 distance: 159 - 160: 41.050 distance: 159 - 165: 21.585 distance: 160 - 183: 26.610 distance: 161 - 162: 27.116 distance: 161 - 163: 43.507 distance: 162 - 164: 30.298