Starting phenix.real_space_refine on Fri Mar 6 05:55:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lnc_0930/03_2026/6lnc_0930.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lnc_0930/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6lnc_0930/03_2026/6lnc_0930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lnc_0930/03_2026/6lnc_0930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lnc_0930/03_2026/6lnc_0930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lnc_0930/03_2026/6lnc_0930.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 6.86, per 1000 atoms: 0.24 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: 2.92 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: 3.27 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: 5.44 Time building geometry restraints manager: 3.88 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: 17404 34.29 - 68.59: 356 68.59 - 102.88: 33 102.88 - 137.17: 1 137.17 - 171.46: 5 Dihedral angle restraints: 17799 sinusoidal: 7697 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 17796 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 29.250 Find NCS groups from input model: 0.430 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 14.414 171.465 11237 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 covalent geometry : bond 0.00867 (29804) covalent geometry : angle 1.16758 (40737) hydrogen bonds : bond 0.17354 ( 816) hydrogen bonds : angle 7.06190 ( 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 : 1.006 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: 0.1767 time to fit residues: 96.6476 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 : 0.948 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4432 r_free = 0.4432 target = 0.227459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.202093 restraints weight = 35303.677| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 1.24 r_work: 0.3835 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29804 Z= 0.124 Angle : 0.634 9.421 40737 Z= 0.338 Chirality : 0.044 0.243 4498 Planarity : 0.006 0.061 4998 Dihedral : 14.540 179.157 4665 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 1.38 % Allowed : 6.90 % Favored : 91.72 % 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: -3.65 (0.12), residues: 3395 helix: -2.25 (0.14), residues: 995 sheet: -1.06 (0.23), residues: 507 loop : -3.02 (0.12), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 240 TYR 0.019 0.001 TYR J 219 PHE 0.024 0.001 PHE J 240 TRP 0.043 0.002 TRP J 203 HIS 0.010 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00267 (29804) covalent geometry : angle 0.63393 (40737) hydrogen bonds : bond 0.04296 ( 816) hydrogen bonds : angle 5.38582 ( 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 346 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 304 time to evaluate : 0.972 Fit side-chains REVERT: G 181 PHE cc_start: 0.7685 (m-80) cc_final: 0.7455 (m-80) REVERT: G 297 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.6313 (p90) REVERT: E 107 LYS cc_start: 0.7749 (tmtt) cc_final: 0.7539 (tmtt) REVERT: E 202 ASP cc_start: 0.6489 (p0) cc_final: 0.6207 (p0) REVERT: D 123 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.6629 (mt) REVERT: D 347 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7324 (p90) REVERT: C 11 ARG cc_start: 0.8786 (ptt-90) cc_final: 0.8438 (ptt-90) REVERT: C 122 LYS cc_start: 0.7668 (tptt) cc_final: 0.7375 (tptt) REVERT: B 107 LYS cc_start: 0.8005 (mppt) cc_final: 0.7798 (mmmt) REVERT: H 125 HIS cc_start: 0.6694 (t-90) cc_final: 0.6462 (t-170) REVERT: H 126 ASP cc_start: 0.6103 (t70) cc_final: 0.5871 (t0) REVERT: H 434 ARG cc_start: 0.5515 (mmt90) cc_final: 0.4821 (mmm160) REVERT: H 557 MET cc_start: 0.5760 (ttp) cc_final: 0.5492 (ttm) REVERT: H 564 MET cc_start: 0.6555 (mmm) cc_final: 0.6125 (mmm) REVERT: A 169 MET cc_start: 0.6236 (tmt) cc_final: 0.5846 (tmm) REVERT: J 215 LEU cc_start: -0.1927 (OUTLIER) cc_final: -0.2191 (pp) REVERT: I 327 GLU cc_start: 0.4455 (pt0) cc_final: 0.4255 (pt0) outliers start: 42 outliers final: 16 residues processed: 336 average time/residue: 0.1786 time to fit residues: 95.7763 Evaluate side-chains 258 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 155 VAL 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 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: 7.9990 chunk 132 optimal weight: 0.0870 chunk 20 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.225632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.168654 restraints weight = 35002.951| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 7.01 r_work: 0.3178 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1857 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= 0.137 Angle : 0.609 9.546 40737 Z= 0.321 Chirality : 0.044 0.256 4498 Planarity : 0.006 0.058 4998 Dihedral : 13.894 176.875 4664 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.07 % Allowed : 8.87 % Favored : 89.06 % 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: -3.17 (0.13), residues: 3395 helix: -1.64 (0.15), residues: 995 sheet: -0.86 (0.23), residues: 503 loop : -2.83 (0.12), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 283 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 covalent geometry : bond 0.00315 (29804) covalent geometry : angle 0.60947 (40737) hydrogen bonds : bond 0.04234 ( 816) hydrogen bonds : angle 5.05641 ( 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 318 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 255 time to evaluate : 1.099 Fit side-chains REVERT: G 181 PHE cc_start: 0.8014 (m-80) cc_final: 0.7661 (m-80) REVERT: G 297 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.5966 (p90) REVERT: E 96 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7825 (mm-30) REVERT: E 107 LYS cc_start: 0.8184 (tmtt) cc_final: 0.7931 (tmtt) REVERT: D 202 ASP cc_start: 0.7760 (p0) cc_final: 0.7538 (p0) REVERT: D 252 ASP cc_start: 0.8128 (m-30) cc_final: 0.7909 (m-30) REVERT: D 347 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7663 (p90) REVERT: C 122 LYS cc_start: 0.7803 (tptt) cc_final: 0.7493 (tptp) REVERT: B 316 TYR cc_start: 0.8303 (m-80) cc_final: 0.7979 (m-80) REVERT: H 434 ARG cc_start: 0.5138 (mmt90) cc_final: 0.4153 (mmm160) REVERT: H 557 MET cc_start: 0.5605 (ttp) cc_final: 0.5232 (ttm) REVERT: A 169 MET cc_start: 0.5107 (tmt) cc_final: 0.4571 (tmm) REVERT: J 215 LEU cc_start: -0.2689 (OUTLIER) cc_final: -0.3051 (pp) REVERT: I 342 MET cc_start: 0.5092 (OUTLIER) cc_final: 0.4393 (ttt) outliers start: 63 outliers final: 32 residues processed: 298 average time/residue: 0.1738 time to fit residues: 83.3177 Evaluate side-chains 273 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 297 TYR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 91 VAL 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 122 LYS 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 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 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 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: 0.9980 chunk 308 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS F 135 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.226031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.168354 restraints weight = 35058.162| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 7.25 r_work: 0.3174 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29804 Z= 0.129 Angle : 0.584 9.263 40737 Z= 0.306 Chirality : 0.043 0.319 4498 Planarity : 0.005 0.054 4998 Dihedral : 13.594 176.261 4664 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.46 % Allowed : 9.76 % 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: -2.81 (0.13), residues: 3395 helix: -1.20 (0.16), residues: 989 sheet: -0.71 (0.23), residues: 503 loop : -2.67 (0.12), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 283 TYR 0.014 0.001 TYR D 275 PHE 0.023 0.001 PHE J 240 TRP 0.026 0.001 TRP J 203 HIS 0.006 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00297 (29804) covalent geometry : angle 0.58449 (40737) hydrogen bonds : bond 0.03906 ( 816) hydrogen bonds : angle 4.85398 ( 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 333 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 258 time to evaluate : 0.989 Fit side-chains REVERT: G 181 PHE cc_start: 0.8087 (m-80) cc_final: 0.7789 (m-80) REVERT: G 297 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.5964 (p90) REVERT: G 315 HIS cc_start: 0.7936 (t-90) cc_final: 0.7564 (t-170) REVERT: E 96 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: D 202 ASP cc_start: 0.7917 (p0) cc_final: 0.7696 (p0) REVERT: D 347 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7667 (p90) REVERT: C 122 LYS cc_start: 0.7748 (tptt) cc_final: 0.7468 (tptt) REVERT: B 107 LYS cc_start: 0.8164 (mppt) cc_final: 0.7642 (mmmt) REVERT: H 434 ARG cc_start: 0.5033 (mmt90) cc_final: 0.3869 (mmm160) REVERT: H 493 GLN cc_start: 0.6313 (mm110) cc_final: 0.3675 (tt0) REVERT: H 564 MET cc_start: 0.6108 (mmm) cc_final: 0.5861 (mmm) REVERT: A 169 MET cc_start: 0.5289 (OUTLIER) cc_final: 0.4705 (tmm) REVERT: I 311 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5123 (mm) REVERT: I 373 PHE cc_start: 0.4685 (OUTLIER) cc_final: 0.4137 (p90) outliers start: 75 outliers final: 35 residues processed: 312 average time/residue: 0.1710 time to fit residues: 85.9043 Evaluate side-chains 279 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 88 SER 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 38 THR Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 96 GLU 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 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 C residue 193 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 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 239 THR 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 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 373 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 134 optimal weight: 0.9990 chunk 277 optimal weight: 0.5980 chunk 210 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 343 optimal weight: 7.9990 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: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 GLN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 311 GLN A 29 HIS ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 237 HIS I 320 ASN I 338 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.228080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.171561 restraints weight = 35379.487| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 6.77 r_work: 0.3185 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29804 Z= 0.107 Angle : 0.550 9.175 40737 Z= 0.288 Chirality : 0.042 0.559 4498 Planarity : 0.005 0.052 4998 Dihedral : 13.410 175.476 4664 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.33 % Allowed : 10.97 % Favored : 86.70 % 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: -2.48 (0.14), residues: 3395 helix: -0.86 (0.17), residues: 989 sheet: -0.54 (0.24), residues: 504 loop : -2.50 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 11 TYR 0.015 0.001 TYR C 275 PHE 0.022 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 covalent geometry : bond 0.00238 (29804) covalent geometry : angle 0.54969 (40737) hydrogen bonds : bond 0.03473 ( 816) hydrogen bonds : angle 4.67041 ( 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 328 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 257 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: G 181 PHE cc_start: 0.8080 (m-80) cc_final: 0.7772 (m-80) REVERT: G 297 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.5877 (p90) REVERT: E 74 ASP cc_start: 0.9059 (m-30) cc_final: 0.8727 (m-30) REVERT: E 96 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: E 122 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7416 (tttp) REVERT: D 97 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8597 (pt) REVERT: D 202 ASP cc_start: 0.7806 (p0) cc_final: 0.7572 (p0) REVERT: D 347 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7669 (p90) REVERT: C 122 LYS cc_start: 0.7690 (tptt) cc_final: 0.7401 (tptt) REVERT: B 107 LYS cc_start: 0.8132 (mppt) cc_final: 0.7573 (mmmt) REVERT: H 83 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6396 (mt0) REVERT: H 436 GLU cc_start: 0.5370 (OUTLIER) cc_final: 0.4961 (pt0) REVERT: H 493 GLN cc_start: 0.6192 (mm110) cc_final: 0.3582 (tt0) REVERT: H 530 GLU cc_start: 0.5168 (pm20) cc_final: 0.4187 (pm20) REVERT: H 557 MET cc_start: 0.5667 (ttp) cc_final: 0.5091 (ptm) REVERT: H 564 MET cc_start: 0.6321 (mmm) cc_final: 0.6088 (mmm) REVERT: A 169 MET cc_start: 0.4884 (OUTLIER) cc_final: 0.4378 (tmm) REVERT: J 228 MET cc_start: 0.3404 (mtp) cc_final: 0.3124 (mtp) REVERT: I 311 LEU cc_start: 0.5619 (OUTLIER) cc_final: 0.4928 (mm) REVERT: I 327 GLU cc_start: 0.2409 (pt0) cc_final: 0.2160 (tm-30) outliers start: 71 outliers final: 46 residues processed: 308 average time/residue: 0.1670 time to fit residues: 83.4729 Evaluate side-chains 290 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 235 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 48 LEU 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 311 GLN Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 96 GLU 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 97 LEU 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 309 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain H residue 15 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 239 THR Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 436 GLU Chi-restraints excluded: chain H residue 448 GLU Chi-restraints excluded: chain H residue 457 VAL 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 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 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 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 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: 9.9990 chunk 48 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 322 optimal weight: 0.0870 chunk 219 optimal weight: 7.9990 chunk 326 optimal weight: 20.0000 chunk 318 optimal weight: 50.0000 chunk 310 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 349 HIS ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 ASN H 562 GLN H 571 HIS ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.217301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.170971 restraints weight = 34772.241| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.79 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29804 Z= 0.188 Angle : 0.638 9.992 40737 Z= 0.330 Chirality : 0.045 0.482 4498 Planarity : 0.005 0.055 4998 Dihedral : 13.414 167.152 4664 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.69 % Allowed : 11.27 % Favored : 86.04 % 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: -2.54 (0.14), residues: 3395 helix: -0.92 (0.17), residues: 986 sheet: -0.63 (0.24), residues: 505 loop : -2.50 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 283 TYR 0.016 0.002 TYR H 622 PHE 0.027 0.002 PHE J 240 TRP 0.024 0.002 TRP J 203 HIS 0.008 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00452 (29804) covalent geometry : angle 0.63850 (40737) hydrogen bonds : bond 0.04449 ( 816) hydrogen bonds : angle 4.79928 ( 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 317 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 235 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: G 297 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.6550 (p90) REVERT: F 97 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8094 (pt) REVERT: E 74 ASP cc_start: 0.8847 (m-30) cc_final: 0.8604 (m-30) REVERT: D 97 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8670 (pt) REVERT: D 277 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.5225 (pp20) REVERT: D 347 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7650 (p90) REVERT: C 155 VAL cc_start: 0.8749 (m) cc_final: 0.8532 (p) REVERT: H 434 ARG cc_start: 0.5994 (mmt90) cc_final: 0.5255 (mmm160) REVERT: H 530 GLU cc_start: 0.5457 (pm20) cc_final: 0.4124 (pm20) REVERT: H 557 MET cc_start: 0.6225 (ttp) cc_final: 0.5891 (ptm) REVERT: H 562 GLN cc_start: 0.5055 (OUTLIER) cc_final: 0.4080 (tm130) REVERT: H 564 MET cc_start: 0.6581 (mmm) cc_final: 0.6178 (mmm) REVERT: A 169 MET cc_start: 0.5805 (OUTLIER) cc_final: 0.5335 (tmm) REVERT: I 311 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6722 (mm) outliers start: 82 outliers final: 55 residues processed: 293 average time/residue: 0.1701 time to fit residues: 80.9237 Evaluate side-chains 286 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 223 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 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 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 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 120 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain B residue 26 ASP 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 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 513 ILE 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 563 LEU Chi-restraints excluded: chain H residue 625 VAL 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 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 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 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: 1.9990 chunk 132 optimal weight: 0.6980 chunk 303 optimal weight: 20.0000 chunk 150 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 chunk 226 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 266 optimal weight: 5.9990 chunk 109 optimal weight: 0.2980 chunk 270 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 GLN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN I 320 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.227978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.202730 restraints weight = 35062.278| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 1.22 r_work: 0.3941 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2666 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= 0.100 Angle : 0.539 9.146 40737 Z= 0.281 Chirality : 0.041 0.356 4498 Planarity : 0.005 0.050 4998 Dihedral : 13.234 165.418 4664 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.43 % Allowed : 11.73 % Favored : 85.84 % 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: -2.23 (0.14), residues: 3395 helix: -0.63 (0.17), residues: 993 sheet: -0.43 (0.24), residues: 510 loop : -2.35 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 283 TYR 0.018 0.001 TYR C 275 PHE 0.022 0.001 PHE J 240 TRP 0.021 0.001 TRP J 203 HIS 0.008 0.001 HIS G 315 Details of bonding type rmsd covalent geometry : bond 0.00217 (29804) covalent geometry : angle 0.53919 (40737) hydrogen bonds : bond 0.03231 ( 816) hydrogen bonds : angle 4.57309 ( 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 322 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 248 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 297 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.5960 (p90) REVERT: F 97 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8202 (pt) REVERT: E 74 ASP cc_start: 0.8759 (m-30) cc_final: 0.8410 (m-30) REVERT: D 97 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8511 (pt) REVERT: D 314 GLU cc_start: 0.7562 (mp0) cc_final: 0.6905 (mm-30) REVERT: D 347 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7634 (p90) REVERT: C 120 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: C 171 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8822 (mp) REVERT: H 530 GLU cc_start: 0.5477 (pm20) cc_final: 0.4148 (pm20) REVERT: H 562 GLN cc_start: 0.5402 (OUTLIER) cc_final: 0.5035 (tm-30) REVERT: H 564 MET cc_start: 0.6600 (mmm) cc_final: 0.6195 (mmm) REVERT: A 169 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6022 (tmm) outliers start: 74 outliers final: 43 residues processed: 299 average time/residue: 0.1652 time to fit residues: 79.2710 Evaluate side-chains 292 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 241 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 38 THR Chi-restraints excluded: chain F residue 97 LEU 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 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 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 B residue 176 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 302 THR 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 219 LEU Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 436 GLU Chi-restraints excluded: chain H residue 448 GLU Chi-restraints excluded: chain H residue 457 VAL 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 563 LEU 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 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 311 LEU Chi-restraints excluded: chain I residue 303 LEU 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: 7.9990 chunk 136 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 289 optimal weight: 8.9990 chunk 326 optimal weight: 9.9990 chunk 214 optimal weight: 0.0980 chunk 296 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 ASN G 114 GLN F 183 ASN E 162 ASN D 214 HIS C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS H 562 GLN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 HIS I 320 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.216405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.170396 restraints weight = 34756.898| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.71 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29804 Z= 0.216 Angle : 0.667 9.303 40737 Z= 0.344 Chirality : 0.046 0.367 4498 Planarity : 0.006 0.079 4998 Dihedral : 13.343 160.859 4664 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.66 % Allowed : 11.96 % 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: -2.44 (0.14), residues: 3395 helix: -0.85 (0.16), residues: 993 sheet: -0.55 (0.24), residues: 508 loop : -2.45 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 283 TYR 0.017 0.002 TYR H 622 PHE 0.028 0.002 PHE C 89 TRP 0.022 0.002 TRP J 203 HIS 0.009 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00522 (29804) covalent geometry : angle 0.66690 (40737) hydrogen bonds : bond 0.04660 ( 816) hydrogen bonds : angle 4.78007 ( 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 309 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 228 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: G 169 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: G 297 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6585 (p90) REVERT: F 97 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8193 (pt) REVERT: E 74 ASP cc_start: 0.8864 (m-30) cc_final: 0.8460 (m-30) REVERT: D 244 ARG cc_start: 0.8527 (ttt180) cc_final: 0.8261 (ttp-170) REVERT: D 277 GLU cc_start: 0.4886 (mp0) cc_final: 0.4556 (mp0) REVERT: D 330 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7670 (m) REVERT: D 347 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.7674 (p90) REVERT: C 155 VAL cc_start: 0.8782 (m) cc_final: 0.8550 (p) REVERT: H 434 ARG cc_start: 0.5998 (mmt90) cc_final: 0.5363 (mmm160) REVERT: H 436 GLU cc_start: 0.4900 (OUTLIER) cc_final: 0.4246 (pt0) REVERT: H 530 GLU cc_start: 0.5445 (pm20) cc_final: 0.4111 (pm20) REVERT: H 564 MET cc_start: 0.6818 (mmm) cc_final: 0.6357 (mmm) REVERT: A 169 MET cc_start: 0.5998 (OUTLIER) cc_final: 0.5417 (tmm) outliers start: 81 outliers final: 55 residues processed: 286 average time/residue: 0.1689 time to fit residues: 78.3611 Evaluate side-chains 281 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 219 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 114 GLN 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 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 311 GLN Chi-restraints excluded: chain F residue 319 VAL 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 57 ILE 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 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 302 THR 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 247 MET Chi-restraints excluded: chain H residue 436 GLU 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 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 I residue 300 LEU Chi-restraints excluded: chain I residue 303 LEU 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: 3.9990 chunk 46 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 283 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 207 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 chunk 309 optimal weight: 30.0000 chunk 35 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN E 69 ASN E 162 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.217129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.170896 restraints weight = 34723.470| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 3.79 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29804 Z= 0.185 Angle : 0.639 9.512 40737 Z= 0.330 Chirality : 0.045 0.380 4498 Planarity : 0.005 0.075 4998 Dihedral : 13.297 161.466 4664 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.60 % Allowed : 12.39 % Favored : 85.02 % 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: -2.45 (0.14), residues: 3395 helix: -0.86 (0.16), residues: 998 sheet: -0.57 (0.24), residues: 508 loop : -2.45 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 286 TYR 0.013 0.002 TYR H 622 PHE 0.032 0.002 PHE I 367 TRP 0.022 0.002 TRP J 203 HIS 0.009 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00443 (29804) covalent geometry : angle 0.63945 (40737) hydrogen bonds : bond 0.04302 ( 816) hydrogen bonds : angle 4.77087 ( 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 308 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 229 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 169 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: G 297 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.6697 (p90) REVERT: F 97 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8154 (pt) REVERT: E 74 ASP cc_start: 0.8841 (m-30) cc_final: 0.8549 (m-30) REVERT: E 340 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.7730 (m-40) REVERT: D 97 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8670 (pt) REVERT: D 244 ARG cc_start: 0.8563 (ttt180) cc_final: 0.8329 (ttp-170) REVERT: D 277 GLU cc_start: 0.4929 (mp0) cc_final: 0.4622 (mp0) REVERT: D 330 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7663 (m) REVERT: C 155 VAL cc_start: 0.8747 (m) cc_final: 0.8523 (p) REVERT: B 14 ASP cc_start: 0.7880 (p0) cc_final: 0.7617 (p0) REVERT: H 434 ARG cc_start: 0.5939 (mmt90) cc_final: 0.5259 (mmm160) REVERT: H 436 GLU cc_start: 0.4765 (OUTLIER) cc_final: 0.4150 (pt0) REVERT: H 530 GLU cc_start: 0.5370 (pm20) cc_final: 0.4033 (pm20) REVERT: H 564 MET cc_start: 0.6769 (mmm) cc_final: 0.6285 (mmm) REVERT: A 169 MET cc_start: 0.5908 (OUTLIER) cc_final: 0.5603 (tmt) outliers start: 79 outliers final: 58 residues processed: 288 average time/residue: 0.1674 time to fit residues: 78.2235 Evaluate side-chains 287 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 221 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 30 THR 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 277 GLU Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 69 ASN 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 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 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 325 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 302 THR 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 247 MET Chi-restraints excluded: chain H residue 436 GLU Chi-restraints excluded: chain H residue 448 GLU Chi-restraints excluded: chain H residue 457 VAL 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 109 VAL Chi-restraints excluded: chain J residue 183 GLU 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 308 GLU Chi-restraints excluded: chain I residue 330 VAL 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 ************** Weight determination summary: number of chunks: 344 random chunks: chunk 133 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 chunk 319 optimal weight: 0.4980 chunk 136 optimal weight: 9.9990 chunk 323 optimal weight: 7.9990 chunk 298 optimal weight: 10.0000 chunk 343 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 339 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.218666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.159911 restraints weight = 34663.585| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 7.61 r_work: 0.3188 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29804 Z= 0.140 Angle : 0.601 8.821 40737 Z= 0.310 Chirality : 0.043 0.360 4498 Planarity : 0.005 0.067 4998 Dihedral : 13.210 162.883 4664 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 2.30 % Allowed : 12.65 % Favored : 85.05 % 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: -2.27 (0.14), residues: 3395 helix: -0.70 (0.17), residues: 1000 sheet: -0.40 (0.24), residues: 510 loop : -2.37 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 286 TYR 0.014 0.001 TYR G 275 PHE 0.028 0.001 PHE I 367 TRP 0.022 0.001 TRP J 203 HIS 0.008 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00329 (29804) covalent geometry : angle 0.60095 (40737) hydrogen bonds : bond 0.03800 ( 816) hydrogen bonds : angle 4.68214 ( 2305) ********************** REFINEMENT MACRO_CYCLE 10 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 293 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 223 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 169 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: G 297 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.6167 (p90) REVERT: F 97 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8447 (pt) REVERT: E 74 ASP cc_start: 0.8991 (m-30) cc_final: 0.8658 (m-30) REVERT: E 340 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.7968 (m-40) REVERT: D 97 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8677 (pt) REVERT: D 277 GLU cc_start: 0.5284 (mp0) cc_final: 0.4924 (mp0) REVERT: D 314 GLU cc_start: 0.8087 (mp0) cc_final: 0.7139 (mm-30) REVERT: D 330 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8041 (m) REVERT: H 434 ARG cc_start: 0.5080 (mmt90) cc_final: 0.4052 (mmm160) REVERT: H 436 GLU cc_start: 0.5119 (OUTLIER) cc_final: 0.4536 (pt0) REVERT: H 530 GLU cc_start: 0.5189 (pm20) cc_final: 0.4174 (pm20) REVERT: A 169 MET cc_start: 0.4909 (OUTLIER) cc_final: 0.4500 (tmt) outliers start: 70 outliers final: 54 residues processed: 278 average time/residue: 0.1690 time to fit residues: 76.0239 Evaluate side-chains 286 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 224 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 30 THR 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 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 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 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 157 THR 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 302 THR 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 247 MET Chi-restraints excluded: chain H residue 436 GLU Chi-restraints excluded: chain H residue 448 GLU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 513 ILE 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 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 183 GLU 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 330 VAL 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 ************** Weight determination summary: number of chunks: 344 random chunks: chunk 314 optimal weight: 50.0000 chunk 179 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 272 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 211 optimal weight: 0.9980 chunk 265 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 chunk 144 optimal weight: 0.0470 chunk 275 optimal weight: 0.0470 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN E 162 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 ASN I 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.223638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.199018 restraints weight = 34885.746| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 1.18 r_work: 0.3806 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 29804 Z= 0.096 Angle : 0.538 9.177 40737 Z= 0.278 Chirality : 0.041 0.277 4498 Planarity : 0.005 0.055 4998 Dihedral : 13.076 167.273 4664 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.84 % Allowed : 13.14 % Favored : 85.02 % 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: -1.96 (0.14), residues: 3395 helix: -0.38 (0.17), residues: 998 sheet: -0.30 (0.24), residues: 510 loop : -2.18 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 240 TYR 0.019 0.001 TYR C 275 PHE 0.024 0.001 PHE A 138 TRP 0.019 0.001 TRP J 203 HIS 0.006 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00207 (29804) covalent geometry : angle 0.53769 (40737) hydrogen bonds : bond 0.02961 ( 816) hydrogen bonds : angle 4.44857 ( 2305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5797.35 seconds wall clock time: 100 minutes 26.39 seconds (6026.39 seconds total)