Starting phenix.real_space_refine on Mon Sep 14 06:16:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lnc_0930/09_2026/6lnc_0930.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lnc_0930/09_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_0930/09_2026/6lnc_0930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lnc_0930/09_2026/6lnc_0930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lnc_0930/09_2026/6lnc_0930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lnc_0930/09_2026/6lnc_0930.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6lnc_0930/09_2026/6lnc_0930.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lnc_0930/09_2026/6lnc_0930.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 151 5.16 5 C 18194 2.51 5 N 4991 2.21 5 O 5542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28937 Number of models: 1 Model: "" Number of chains: 11 Chain: "M" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1276 Classifications: {'RNAv2': 60} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 13, 'rna3p_pur': 22, 'rna3p_pyr': 17} Link IDs: {'rna2p': 21, 'rna3p': 38} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 6.05, per 1000 atoms: 0.21 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 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: 3.11 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: 4.95 Time building geometry restraints manager: 3.08 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=" O3' C M 37 " pdb=" P C M 38 " ideal model delta sigma weight residual 1.607 1.634 -0.027 1.20e-02 6.94e+03 4.98e+00 ... (remaining 29799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 39595 3.14 - 6.28: 964 6.28 - 9.42: 145 9.42 - 12.57: 25 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 113.80 101.27 12.53 2.00e+00 2.50e-01 3.92e+01 angle pdb=" C3' G M 15 " pdb=" C2' G M 15 " pdb=" O2' G M 15 " ideal model delta sigma weight residual 109.80 121.44 -11.64 2.00e+00 2.50e-01 3.39e+01 ... (remaining 40732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.54: 17031 28.54 - 57.08: 493 57.08 - 85.62: 40 85.62 - 114.16: 0 114.16 - 142.70: 3 Dihedral angle restraints: 17567 sinusoidal: 7465 harmonic: 10102 Sorted by residual: dihedral pdb=" C4' U M 54 " pdb=" C3' U M 54 " pdb=" C2' U M 54 " pdb=" C1' U M 54 " ideal model delta sinusoidal sigma weight residual 36.34 -37.83 74.17 1 3.10e+00 1.04e-01 7.26e+02 dihedral pdb=" C4' A M 45 " pdb=" C3' A M 45 " pdb=" C2' A M 45 " pdb=" C1' A M 45 " ideal model delta sinusoidal sigma weight residual 36.34 -35.32 71.67 1 3.10e+00 1.04e-01 6.85e+02 dihedral pdb=" C4' U M 42 " pdb=" C3' U M 42 " pdb=" C2' U M 42 " pdb=" C1' U M 42 " ideal model delta sinusoidal sigma weight residual 36.35 -34.66 71.00 1 3.10e+00 1.04e-01 6.74e+02 ... (remaining 17564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3973 0.110 - 0.221: 440 0.221 - 0.331: 68 0.331 - 0.441: 14 0.441 - 0.552: 3 Chirality restraints: 4498 Sorted by residual: chirality pdb=" C2' G M 15 " pdb=" C3' G M 15 " pdb=" O2' G M 15 " pdb=" C1' G M 15 " both_signs ideal model delta sigma weight residual False -2.79 -2.24 -0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" C3' G M 15 " pdb=" C4' G M 15 " pdb=" O3' G M 15 " pdb=" C2' G M 15 " both_signs ideal model delta sigma weight residual False -2.50 -3.02 0.52 2.00e-01 2.50e+01 6.70e+00 chirality pdb=" C2' G M 26 " pdb=" C3' G M 26 " pdb=" O2' G M 26 " pdb=" C1' G M 26 " both_signs ideal model delta sigma weight residual False -2.79 -2.34 -0.45 2.00e-01 2.50e+01 5.11e+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: 1.260 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.880 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 29804 Z= 0.363 Angle : 1.198 15.706 40737 Z= 0.626 Chirality : 0.077 0.552 4498 Planarity : 0.009 0.080 4998 Dihedral : 12.990 142.696 11005 Min Nonbonded Distance : 1.550 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 0.20 % Allowed : 4.43 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.69 (0.11), residues: 3395 helix: -3.57 (0.10), residues: 955 sheet: -1.39 (0.23), residues: 500 loop : -3.49 (0.11), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG E 283 TYR 0.057 0.004 TYR E 9 PHE 0.055 0.004 PHE C 89 TRP 0.085 0.004 TRP J 203 HIS 0.019 0.003 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00867 / 0.36 (29804) covalent geometry : angle 1.19842 / 0.63 (40737) hydrogen bonds : bond 0.17354 / 8.94 ( 816) hydrogen bonds : angle 7.06190 / 2.89 ( 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 : 0.872 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: 0.1872 time to fit residues: 102.7886 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 : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 179 GLN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS F 145 ASN F 214 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN E 153 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.229241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.202302 restraints weight = 35388.456| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 1.31 r_work: 0.3869 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1546 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= 0.126 Angle : 0.754 12.767 40737 Z= 0.362 Chirality : 0.060 0.774 4498 Planarity : 0.006 0.061 4998 Dihedral : 10.802 149.515 4433 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.31 % Allowed : 7.00 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.12), residues: 3395 helix: -2.23 (0.14), residues: 989 sheet: -1.07 (0.23), residues: 515 loop : -2.98 (0.12), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 240 TYR 0.020 0.001 TYR J 219 PHE 0.024 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/Z covalent geometry : bond 0.00272 / 0.13 (29804) covalent geometry : angle 0.75441 / 0.36 (40737) hydrogen bonds : bond 0.04327 / 2.25 ( 816) hydrogen bonds : angle 5.41070 / 2.25 ( 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 340 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 1.303 Fit side-chains REVERT: G 181 PHE cc_start: 0.7839 (m-80) cc_final: 0.7582 (m-80) REVERT: G 297 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.6348 (p90) REVERT: E 107 LYS cc_start: 0.7834 (tmtt) cc_final: 0.7611 (tmtt) REVERT: E 202 ASP cc_start: 0.7029 (p0) cc_final: 0.6756 (p0) REVERT: D 123 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.6710 (mt) REVERT: D 347 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7355 (p90) REVERT: C 11 ARG cc_start: 0.8789 (ptt-90) cc_final: 0.8471 (ptt-90) REVERT: B 107 LYS cc_start: 0.8096 (mppt) cc_final: 0.7848 (mmmt) REVERT: H 125 HIS cc_start: 0.6762 (t-90) cc_final: 0.6498 (t-170) REVERT: H 126 ASP cc_start: 0.6290 (t70) cc_final: 0.5915 (t0) REVERT: H 434 ARG cc_start: 0.5514 (mmt90) cc_final: 0.4713 (mmm160) REVERT: H 557 MET cc_start: 0.6022 (ttp) cc_final: 0.5705 (ttm) REVERT: H 564 MET cc_start: 0.6689 (mmm) cc_final: 0.6282 (mmm) REVERT: A 169 MET cc_start: 0.6410 (tmt) cc_final: 0.5925 (tmm) REVERT: J 215 LEU cc_start: -0.1963 (OUTLIER) cc_final: -0.2227 (pp) outliers start: 40 outliers final: 16 residues processed: 331 average time/residue: 0.1936 time to fit residues: 102.7943 Evaluate side-chains 254 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain F residue 26 ASP 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: 2.9990 chunk 132 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 chunk 218 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 281 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS D 218 ASN C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN B 77 HIS ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 581 ASN A 32 ASN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 HIS ** I 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.217508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.159281 restraints weight = 34911.048| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 6.75 r_work: 0.3166 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 29804 Z= 0.232 Angle : 0.820 15.004 40737 Z= 0.396 Chirality : 0.064 0.658 4498 Planarity : 0.006 0.063 4998 Dihedral : 11.229 161.026 4432 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.30 % Allowed : 9.20 % Favored : 88.50 % 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: -3.32 (0.13), residues: 3395 helix: -1.83 (0.15), residues: 995 sheet: -0.99 (0.23), residues: 505 loop : -2.87 (0.12), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 283 TYR 0.020 0.002 TYR J 219 PHE 0.031 0.002 PHE C 89 TRP 0.035 0.002 TRP J 203 HIS 0.008 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 (29804) covalent geometry : angle 0.82044 / 0.40 (40737) hydrogen bonds : bond 0.05295 / 2.73 ( 816) hydrogen bonds : angle 5.27575 / 2.17 ( 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 311 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 241 time to evaluate : 1.094 Fit side-chains REVERT: G 181 PHE cc_start: 0.8116 (m-80) cc_final: 0.7773 (m-80) REVERT: G 297 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.6408 (p90) REVERT: E 96 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7885 (mm-30) REVERT: D 252 ASP cc_start: 0.8109 (m-30) cc_final: 0.7894 (m-30) REVERT: D 347 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7739 (p90) REVERT: C 155 VAL cc_start: 0.8915 (m) cc_final: 0.8668 (p) REVERT: B 107 LYS cc_start: 0.8131 (mppt) cc_final: 0.7540 (mmmt) REVERT: B 318 GLU cc_start: 0.6935 (pt0) cc_final: 0.6709 (mt-10) REVERT: H 434 ARG cc_start: 0.5473 (mmt90) cc_final: 0.4395 (mmm160) REVERT: H 493 GLN cc_start: 0.6519 (mm110) cc_final: 0.3987 (tt0) REVERT: H 530 GLU cc_start: 0.5185 (pm20) cc_final: 0.4115 (pm20) REVERT: H 557 MET cc_start: 0.5368 (ttp) cc_final: 0.4982 (ttm) REVERT: I 323 MET cc_start: 0.3885 (mmm) cc_final: 0.3491 (mmm) REVERT: I 342 MET cc_start: 0.4655 (OUTLIER) cc_final: 0.4134 (ttt) outliers start: 70 outliers final: 43 residues processed: 291 average time/residue: 0.1857 time to fit residues: 87.8114 Evaluate side-chains 277 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 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 91 VAL Chi-restraints excluded: chain F residue 319 VAL 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 E residue 193 MET Chi-restraints excluded: chain E residue 296 CYS 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 157 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain B residue 26 ASP 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 239 THR Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 436 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 568 VAL 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 304 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: 1.9990 chunk 308 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS F 135 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 HIS H 581 ASN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 237 HIS I 252 HIS I 320 ASN ** I 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.230255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.204135 restraints weight = 35496.642| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 1.21 r_work: 0.3894 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29804 Z= 0.107 Angle : 0.636 9.284 40737 Z= 0.311 Chirality : 0.050 0.430 4498 Planarity : 0.005 0.067 4998 Dihedral : 10.720 163.792 4432 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.17 % Allowed : 10.51 % Favored : 87.32 % 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: -2.79 (0.13), residues: 3395 helix: -1.23 (0.16), residues: 993 sheet: -0.61 (0.23), residues: 505 loop : -2.66 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 538 TYR 0.018 0.001 TYR C 275 PHE 0.022 0.001 PHE J 240 TRP 0.025 0.001 TRP J 203 HIS 0.007 0.001 HIS G 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (29804) covalent geometry : angle 0.63611 / 0.31 (40737) hydrogen bonds : bond 0.03475 / 1.81 ( 816) hydrogen bonds : angle 4.86192 / 2.02 ( 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 330 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 264 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: G 297 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.6198 (p90) REVERT: E 122 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7395 (tttp) REVERT: D 97 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8434 (pt) REVERT: D 202 ASP cc_start: 0.7735 (p0) cc_final: 0.7395 (p0) REVERT: D 347 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7490 (p90) REVERT: H 448 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6790 (pp20) REVERT: H 557 MET cc_start: 0.6325 (ttp) cc_final: 0.6080 (ttm) REVERT: H 564 MET cc_start: 0.6630 (mmm) cc_final: 0.6405 (mmm) REVERT: A 14 LEU cc_start: 0.5015 (OUTLIER) cc_final: 0.4751 (tm) REVERT: A 169 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.5994 (tmm) REVERT: I 311 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6899 (mm) outliers start: 66 outliers final: 26 residues processed: 312 average time/residue: 0.1919 time to fit residues: 96.9594 Evaluate side-chains 273 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 249 THR 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 69 ASN Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 122 LYS 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 120 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 83 GLN Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 448 GLU 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 14 LEU Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 333 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 134 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 343 optimal weight: 10.0000 chunk 281 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS D 214 HIS ** 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** A 29 HIS ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN I 320 ASN I 338 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.217028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.171655 restraints weight = 34931.651| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.76 r_work: 0.3188 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 29804 Z= 0.232 Angle : 0.785 14.844 40737 Z= 0.379 Chirality : 0.061 0.658 4498 Planarity : 0.006 0.072 4998 Dihedral : 11.055 164.804 4432 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.73 % Allowed : 11.30 % Favored : 85.97 % 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: -2.84 (0.13), residues: 3395 helix: -1.26 (0.16), residues: 1001 sheet: -0.77 (0.23), residues: 509 loop : -2.66 (0.13), residues: 1885 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 0.030 0.002 PHE C 89 TRP 0.024 0.002 TRP J 203 HIS 0.008 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (29804) covalent geometry : angle 0.78461 / 0.38 (40737) hydrogen bonds : bond 0.05016 / 2.59 ( 816) hydrogen bonds : angle 5.01647 / 2.06 ( 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 321 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 238 time to evaluate : 1.116 Fit side-chains REVERT: G 169 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: G 297 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.6490 (p90) REVERT: F 97 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8512 (pt) REVERT: D 97 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8670 (pt) REVERT: D 277 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5512 (pp20) REVERT: D 347 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7770 (p90) REVERT: C 155 VAL cc_start: 0.8943 (m) cc_final: 0.8705 (p) REVERT: H 434 ARG cc_start: 0.5379 (mmt90) cc_final: 0.4289 (mmm160) REVERT: H 448 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7427 (pp20) REVERT: H 493 GLN cc_start: 0.6232 (mm110) cc_final: 0.3768 (tt0) REVERT: H 530 GLU cc_start: 0.5074 (pm20) cc_final: 0.4078 (pm20) REVERT: H 557 MET cc_start: 0.5448 (ttp) cc_final: 0.5070 (ttm) REVERT: H 564 MET cc_start: 0.6502 (mmm) cc_final: 0.6128 (mmm) REVERT: J 78 LEU cc_start: 0.6185 (mp) cc_final: 0.5867 (mp) REVERT: J 94 ILE cc_start: 0.5791 (OUTLIER) cc_final: 0.5588 (tt) REVERT: I 311 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5460 (mm) outliers start: 83 outliers final: 59 residues processed: 300 average time/residue: 0.1882 time to fit residues: 92.1862 Evaluate side-chains 295 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 227 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 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 193 MET Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain 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 89 PHE 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 220 MET Chi-restraints excluded: chain C residue 331 ILE 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 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 494 ASP Chi-restraints excluded: chain H residue 513 ILE Chi-restraints excluded: chain H residue 534 ILE 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 42 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain I residue 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: 10.0000 chunk 48 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 110 optimal weight: 0.0030 chunk 322 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 326 optimal weight: 9.9990 chunk 318 optimal weight: 40.0000 chunk 310 optimal weight: 40.0000 chunk 294 optimal weight: 10.0000 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 GLN G 315 HIS F 99 GLN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 571 HIS ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.220408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.194788 restraints weight = 34939.169| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 1.20 r_work: 0.3773 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29804 Z= 0.136 Angle : 0.666 10.271 40737 Z= 0.323 Chirality : 0.053 0.505 4498 Planarity : 0.005 0.060 4998 Dihedral : 10.864 167.151 4432 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.79 % Allowed : 11.73 % Favored : 85.48 % 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: -2.58 (0.14), residues: 3395 helix: -1.00 (0.16), residues: 997 sheet: -0.54 (0.24), residues: 506 loop : -2.54 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 286 TYR 0.014 0.001 TYR C 275 PHE 0.025 0.001 PHE J 240 TRP 0.022 0.001 TRP J 203 HIS 0.007 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (29804) covalent geometry : angle 0.66582 / 0.32 (40737) hydrogen bonds : bond 0.03898 / 2.02 ( 816) hydrogen bonds : angle 4.78974 / 1.98 ( 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 325 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 240 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: G 297 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.6664 (p90) REVERT: F 97 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8281 (pt) REVERT: E 74 ASP cc_start: 0.8746 (m-30) cc_final: 0.8476 (m-30) REVERT: E 340 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.7653 (m-40) REVERT: D 97 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8557 (pt) REVERT: D 277 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.5286 (pp20) REVERT: D 330 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7835 (m) REVERT: D 347 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7592 (p90) REVERT: H 434 ARG cc_start: 0.5771 (mmt90) cc_final: 0.4896 (mmm160) REVERT: H 448 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6956 (pp20) REVERT: H 530 GLU cc_start: 0.5572 (pm20) cc_final: 0.4236 (pm20) REVERT: H 557 MET cc_start: 0.6474 (ttp) cc_final: 0.6212 (ttm) REVERT: H 564 MET cc_start: 0.6864 (mmm) cc_final: 0.6159 (mmm) REVERT: A 169 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5716 (tmm) REVERT: J 78 LEU cc_start: 0.7618 (mp) cc_final: 0.7159 (mp) REVERT: J 94 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.6922 (tt) REVERT: I 302 GLU cc_start: 0.6464 (mm-30) cc_final: 0.6146 (mm-30) REVERT: I 345 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6455 (tt0) outliers start: 85 outliers final: 52 residues processed: 298 average time/residue: 0.1890 time to fit residues: 91.4657 Evaluate side-chains 285 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 222 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 277 GLU 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 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 176 THR Chi-restraints excluded: chain B residue 210 ARG 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 236 SER Chi-restraints excluded: chain H residue 247 MET Chi-restraints excluded: chain H residue 448 GLU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 513 ILE Chi-restraints excluded: chain H residue 534 ILE Chi-restraints excluded: chain H residue 561 HIS 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 94 ILE Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain I residue 345 GLN Chi-restraints excluded: chain I residue 373 PHE Chi-restraints excluded: chain I residue 377 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 133 optimal weight: 0.9990 chunk 132 optimal weight: 0.4980 chunk 303 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 187 optimal weight: 0.8980 chunk 266 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 270 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 114 GLN G 315 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** 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 = 0.4358 r_free = 0.4358 target = 0.222015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.165116 restraints weight = 35026.295| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 6.95 r_work: 0.3261 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29804 Z= 0.118 Angle : 0.626 9.046 40737 Z= 0.305 Chirality : 0.050 0.456 4498 Planarity : 0.005 0.052 4998 Dihedral : 10.716 171.313 4432 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.73 % Allowed : 12.16 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.14), residues: 3395 helix: -0.76 (0.17), residues: 996 sheet: -0.42 (0.24), residues: 511 loop : -2.42 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 220 TYR 0.015 0.001 TYR C 275 PHE 0.024 0.001 PHE J 240 TRP 0.020 0.001 TRP J 203 HIS 0.006 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (29804) covalent geometry : angle 0.62621 / 0.31 (40737) hydrogen bonds : bond 0.03566 / 1.85 ( 816) hydrogen bonds : angle 4.63057 / 1.91 ( 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 315 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 232 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: G 169 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: G 297 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.6165 (p90) REVERT: F 314 GLU cc_start: 0.7951 (mp0) cc_final: 0.7638 (mp0) REVERT: E 74 ASP cc_start: 0.8962 (m-30) cc_final: 0.8588 (m-30) REVERT: E 122 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7335 (tttp) REVERT: E 340 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.7835 (m-40) REVERT: D 97 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8622 (pt) REVERT: D 330 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.8060 (m) REVERT: C 74 ASP cc_start: 0.8355 (m-30) cc_final: 0.8149 (m-30) REVERT: H 434 ARG cc_start: 0.5270 (mmt90) cc_final: 0.4115 (mmm160) REVERT: H 436 GLU cc_start: 0.5293 (OUTLIER) cc_final: 0.4993 (pt0) REVERT: H 448 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6879 (pp20) REVERT: H 530 GLU cc_start: 0.5207 (pm20) cc_final: 0.4198 (pm20) REVERT: H 557 MET cc_start: 0.5399 (ttp) cc_final: 0.5130 (ttm) REVERT: A 169 MET cc_start: 0.4563 (OUTLIER) cc_final: 0.3969 (tmm) REVERT: J 291 GLU cc_start: 0.5372 (OUTLIER) cc_final: 0.5031 (tm-30) outliers start: 83 outliers final: 56 residues processed: 293 average time/residue: 0.1917 time to fit residues: 91.1508 Evaluate side-chains 288 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 274 TRP Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain 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 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 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 561 HIS 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 184 TYR 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 291 GLU Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain I residue 373 PHE Chi-restraints excluded: chain I residue 377 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 156 optimal weight: 3.9990 chunk 310 optimal weight: 40.0000 chunk 330 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 289 optimal weight: 9.9990 chunk 326 optimal weight: 9.9990 chunk 214 optimal weight: 50.0000 chunk 296 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 315 HIS ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 HIS H 64 GLN ** 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 = 0.4296 r_free = 0.4296 target = 0.215253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.164563 restraints weight = 34906.115| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 4.41 r_work: 0.3157 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 29804 Z= 0.295 Angle : 0.846 15.273 40737 Z= 0.407 Chirality : 0.067 0.795 4498 Planarity : 0.006 0.064 4998 Dihedral : 11.383 165.547 4432 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 3.06 % Allowed : 12.25 % Favored : 84.69 % 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: -2.65 (0.13), residues: 3395 helix: -1.08 (0.16), residues: 987 sheet: -0.62 (0.24), residues: 513 loop : -2.56 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 283 TYR 0.018 0.002 TYR F 175 PHE 0.033 0.002 PHE C 89 TRP 0.023 0.002 TRP E 152 HIS 0.008 0.002 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.30 (29804) covalent geometry : angle 0.84615 / 0.41 (40737) hydrogen bonds : bond 0.05480 / 2.83 ( 816) hydrogen bonds : angle 5.01073 / 2.05 ( 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 319 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 226 time to evaluate : 1.064 Fit side-chains REVERT: G 169 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: G 297 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.6626 (p90) REVERT: G 346 MET cc_start: 0.7282 (mmm) cc_final: 0.7036 (mmm) REVERT: F 97 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8559 (pt) REVERT: E 340 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.7966 (m-40) REVERT: D 97 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8788 (pt) REVERT: D 244 ARG cc_start: 0.8868 (ttt180) cc_final: 0.8642 (ttp-170) REVERT: D 330 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8072 (m) REVERT: C 155 VAL cc_start: 0.8932 (m) cc_final: 0.8694 (p) REVERT: C 334 MET cc_start: 0.8708 (mmm) cc_final: 0.8370 (mmp) REVERT: H 434 ARG cc_start: 0.5584 (mmt90) cc_final: 0.4446 (mmm160) REVERT: H 530 GLU cc_start: 0.5201 (pm20) cc_final: 0.4088 (pm20) REVERT: H 557 MET cc_start: 0.5481 (ttp) cc_final: 0.5229 (ttm) REVERT: A 169 MET cc_start: 0.5032 (OUTLIER) cc_final: 0.4768 (tmt) REVERT: J 291 GLU cc_start: 0.5333 (OUTLIER) cc_final: 0.4940 (tm-30) outliers start: 93 outliers final: 66 residues processed: 298 average time/residue: 0.1919 time to fit residues: 92.7268 Evaluate side-chains 293 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 219 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 274 TRP Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 245 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 87 CYS Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 108 VAL 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 220 MET Chi-restraints excluded: chain B residue 97 LEU 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 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 494 ASP 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 42 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 291 GLU Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain I residue 373 PHE Chi-restraints excluded: chain I residue 377 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 37 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 283 optimal weight: 30.0000 chunk 60 optimal weight: 0.6980 chunk 207 optimal weight: 6.9990 chunk 266 optimal weight: 0.0050 chunk 309 optimal weight: 40.0000 chunk 35 optimal weight: 4.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 315 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 ASN I 320 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.222232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.197528 restraints weight = 34942.791| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 1.16 r_work: 0.3799 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29804 Z= 0.109 Angle : 0.631 9.484 40737 Z= 0.309 Chirality : 0.050 0.565 4498 Planarity : 0.005 0.052 4998 Dihedral : 10.847 168.935 4432 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.33 % Allowed : 13.21 % Favored : 84.46 % 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: -2.25 (0.14), residues: 3395 helix: -0.70 (0.17), residues: 992 sheet: -0.39 (0.24), residues: 517 loop : -2.35 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 240 TYR 0.018 0.001 TYR C 275 PHE 0.025 0.001 PHE I 367 TRP 0.020 0.001 TRP D 143 HIS 0.009 0.001 HIS G 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (29804) covalent geometry : angle 0.63132 / 0.31 (40737) hydrogen bonds : bond 0.03390 / 1.76 ( 816) hydrogen bonds : angle 4.63188 / 1.92 ( 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 309 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 238 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 297 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.6510 (p90) REVERT: F 97 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8116 (pt) REVERT: E 74 ASP cc_start: 0.8629 (m-30) cc_final: 0.8315 (m-30) REVERT: E 340 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.7702 (m-40) REVERT: D 97 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8427 (pt) REVERT: D 244 ARG cc_start: 0.8586 (ttt180) cc_final: 0.8233 (ttp-170) REVERT: D 330 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7561 (m) REVERT: H 125 HIS cc_start: 0.6734 (t-90) cc_final: 0.6507 (t70) REVERT: H 211 ILE cc_start: 0.6028 (mm) cc_final: 0.5638 (mm) REVERT: H 448 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6514 (pp20) REVERT: H 510 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7253 (mttm) REVERT: H 530 GLU cc_start: 0.5355 (pm20) cc_final: 0.4063 (pm20) REVERT: H 557 MET cc_start: 0.6133 (ttp) cc_final: 0.5870 (ttm) REVERT: H 564 MET cc_start: 0.6201 (mmm) cc_final: 0.5906 (mmm) outliers start: 71 outliers final: 53 residues processed: 286 average time/residue: 0.1900 time to fit residues: 88.4824 Evaluate side-chains 290 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 231 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 274 TRP Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 277 GLU 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 51 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 346 MET 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 89 PHE Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 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 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 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 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 66 ASN 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 311 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 133 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 319 optimal weight: 8.9990 chunk 136 optimal weight: 0.0170 chunk 323 optimal weight: 9.9990 chunk 298 optimal weight: 20.0000 chunk 343 optimal weight: 8.9990 chunk 77 optimal weight: 0.2980 chunk 197 optimal weight: 0.0980 chunk 339 optimal weight: 3.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 183 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 ASN I 320 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.222166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.165954 restraints weight = 34798.645| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 6.52 r_work: 0.3258 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2919 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= 0.113 Angle : 0.633 9.016 40737 Z= 0.309 Chirality : 0.050 0.531 4498 Planarity : 0.005 0.056 4998 Dihedral : 10.718 171.091 4432 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.14 % Allowed : 13.50 % Favored : 84.36 % 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: -2.09 (0.14), residues: 3395 helix: -0.56 (0.17), residues: 997 sheet: -0.27 (0.24), residues: 514 loop : -2.26 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 240 TYR 0.015 0.001 TYR D 275 PHE 0.030 0.001 PHE I 367 TRP 0.018 0.001 TRP J 203 HIS 0.007 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (29804) covalent geometry : angle 0.63302 / 0.31 (40737) hydrogen bonds : bond 0.03475 / 1.80 ( 816) hydrogen bonds : angle 4.53630 / 1.88 ( 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 296 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 231 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 169 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: G 297 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.6277 (p90) REVERT: F 97 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8340 (pt) REVERT: F 144 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8071 (ptpt) REVERT: E 74 ASP cc_start: 0.8966 (m-30) cc_final: 0.8593 (m-30) REVERT: E 334 MET cc_start: 0.8233 (mtm) cc_final: 0.7987 (mmm) REVERT: E 340 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.7788 (m-40) REVERT: D 97 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8632 (pt) REVERT: D 244 ARG cc_start: 0.8721 (ttt180) cc_final: 0.8438 (ttp-170) REVERT: D 252 ASP cc_start: 0.8207 (m-30) cc_final: 0.7936 (m-30) REVERT: D 330 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8093 (m) REVERT: H 434 ARG cc_start: 0.4943 (mmt90) cc_final: 0.3862 (mmm160) REVERT: H 436 GLU cc_start: 0.5240 (OUTLIER) cc_final: 0.4791 (pt0) REVERT: H 448 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6856 (pp20) REVERT: H 510 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7228 (mttm) REVERT: H 530 GLU cc_start: 0.5158 (pm20) cc_final: 0.4172 (pm20) REVERT: H 557 MET cc_start: 0.5315 (ttp) cc_final: 0.4590 (ptm) REVERT: J 78 LEU cc_start: 0.6104 (mp) cc_final: 0.5841 (mp) REVERT: I 302 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6867 (mm-30) outliers start: 65 outliers final: 52 residues processed: 282 average time/residue: 0.1935 time to fit residues: 88.2972 Evaluate side-chains 289 residues out of total 3052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 228 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 274 TRP Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 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 51 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 346 MET 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 120 GLU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 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 513 ILE Chi-restraints excluded: chain H residue 534 ILE 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 193 PHE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 66 ASN 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 311 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: 40.0000 chunk 179 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 272 optimal weight: 20.0000 chunk 52 optimal weight: 0.6980 chunk 211 optimal weight: 5.9990 chunk 265 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 144 optimal weight: 0.0050 chunk 275 optimal weight: 5.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN H 125 HIS ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.224218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.199762 restraints weight = 34996.888| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.18 r_work: 0.3842 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29804 Z= 0.101 Angle : 0.605 8.779 40737 Z= 0.295 Chirality : 0.048 0.491 4498 Planarity : 0.005 0.060 4998 Dihedral : 10.556 172.792 4432 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.14 % Allowed : 13.40 % Favored : 84.46 % 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: -1.90 (0.14), residues: 3395 helix: -0.35 (0.17), residues: 989 sheet: -0.27 (0.24), residues: 516 loop : -2.13 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 240 TYR 0.018 0.001 TYR C 275 PHE 0.022 0.001 PHE J 240 TRP 0.018 0.001 TRP J 203 HIS 0.006 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (29804) covalent geometry : angle 0.60485 / 0.30 (40737) hydrogen bonds : bond 0.03172 / 1.65 ( 816) hydrogen bonds : angle 4.43350 / 1.84 ( 2305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6944.59 seconds wall clock time: 120 minutes 8.11 seconds (7208.11 seconds total)