Starting phenix.real_space_refine on Thu Nov 20 00:46:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u0a_8478/11_2025/5u0a_8478.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u0a_8478/11_2025/5u0a_8478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5u0a_8478/11_2025/5u0a_8478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u0a_8478/11_2025/5u0a_8478.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5u0a_8478/11_2025/5u0a_8478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u0a_8478/11_2025/5u0a_8478.map" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 0.017 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 143 5.49 5 S 46 5.16 5 C 17670 2.51 5 N 5313 2.21 5 O 5751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28923 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1439 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 182} Chain breaks: 8 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3980 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 41, 'TRANS': 461} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2017 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain breaks: 1 Chain: "E" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2840 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 15, 'TRANS': 351} Chain: "F" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2840 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 15, 'TRANS': 351} Chain: "G" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2829 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain: "H" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2829 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain: "I" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2543 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1388 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 2 Chain: "K" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1267 Classifications: {'RNA': 59} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 25, 'rna3p_pyr': 13} Link IDs: {'rna2p': 21, 'rna3p': 37} Chain breaks: 1 Chain: "L" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1322 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1013 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "N" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1896 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 20, 'TRANS': 220} Chain breaks: 1 Chain: "O" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 720 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain breaks: 1 Time building chain proxies: 6.80, per 1000 atoms: 0.24 Number of scatterers: 28923 At special positions: 0 Unit cell: (188.19, 131.61, 145.14, 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 46 16.00 P 143 15.00 O 5751 8.00 N 5313 7.00 C 17670 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: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6254 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 32 sheets defined 45.9% alpha, 17.7% beta 28 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 198 through 209 Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.630A pdb=" N GLY A 217 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.832A pdb=" N ARG C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 Processing helix chain 'C' and resid 89 through 105 Processing helix chain 'C' and resid 108 through 119 removed outlier: 3.673A pdb=" N VAL C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 123 removed outlier: 3.842A pdb=" N PHE C 123 " --> pdb=" O SER C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.986A pdb=" N GLU C 141 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 142' Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 227 through 235 removed outlier: 3.567A pdb=" N SER C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.721A pdb=" N HIS C 343 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 359 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.078A pdb=" N SER C 371 " --> pdb=" O GLU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 407 removed outlier: 4.517A pdb=" N ARG C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 446 Processing helix chain 'C' and resid 464 through 487 removed outlier: 3.773A pdb=" N HIS C 468 " --> pdb=" O PRO C 464 " (cutoff:3.500A) Proline residue: C 479 - end of helix Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.609A pdb=" N VAL C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 520 Processing helix chain 'C' and resid 522 through 534 Processing helix chain 'C' and resid 535 through 538 removed outlier: 3.721A pdb=" N SER C 538 " --> pdb=" O THR C 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 535 through 538' Processing helix chain 'D' and resid 39 through 55 Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 248 through 266 Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 310 through 329 Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 355 through 368 removed outlier: 3.647A pdb=" N PHE D 368 " --> pdb=" O VAL D 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 56 removed outlier: 3.502A pdb=" N TRP E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.788A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.938A pdb=" N HIS E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 144 removed outlier: 3.857A pdb=" N LYS E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE E 156 " --> pdb=" O PRO E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 248 through 266 Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 309 through 329 removed outlier: 4.242A pdb=" N ARG E 313 " --> pdb=" O GLY E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 350 removed outlier: 3.588A pdb=" N LEU E 349 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY E 350 " --> pdb=" O ALA E 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 346 through 350' Processing helix chain 'E' and resid 355 through 368 Processing helix chain 'F' and resid 39 through 56 removed outlier: 3.501A pdb=" N TRP F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 76 removed outlier: 3.719A pdb=" N GLU F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 121 through 134 removed outlier: 3.939A pdb=" N HIS F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 144 removed outlier: 3.858A pdb=" N LYS F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE F 156 " --> pdb=" O PRO F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 171 Processing helix chain 'F' and resid 239 through 247 Processing helix chain 'F' and resid 248 through 266 Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 309 through 329 removed outlier: 4.244A pdb=" N ARG F 313 " --> pdb=" O GLY F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 350 removed outlier: 3.588A pdb=" N LEU F 349 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 350 " --> pdb=" O ALA F 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 346 through 350' Processing helix chain 'F' and resid 355 through 368 Processing helix chain 'G' and resid 39 through 56 removed outlier: 3.502A pdb=" N TRP G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 76 removed outlier: 3.720A pdb=" N GLU G 68 " --> pdb=" O ARG G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 Processing helix chain 'G' and resid 121 through 134 removed outlier: 3.938A pdb=" N HIS G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 144 removed outlier: 3.858A pdb=" N LYS G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE G 156 " --> pdb=" O PRO G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 171 Processing helix chain 'G' and resid 239 through 247 Processing helix chain 'G' and resid 248 through 266 Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 309 through 329 removed outlier: 4.244A pdb=" N ARG G 313 " --> pdb=" O GLY G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 350 removed outlier: 3.587A pdb=" N LEU G 349 " --> pdb=" O LEU G 346 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY G 350 " --> pdb=" O ALA G 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 346 through 350' Processing helix chain 'G' and resid 355 through 367 Processing helix chain 'H' and resid 39 through 56 removed outlier: 3.501A pdb=" N TRP H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.720A pdb=" N GLU H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.939A pdb=" N HIS H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 144 removed outlier: 3.857A pdb=" N LYS H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE H 156 " --> pdb=" O PRO H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 171 Processing helix chain 'H' and resid 239 through 247 Processing helix chain 'H' and resid 248 through 266 Processing helix chain 'H' and resid 271 through 276 Processing helix chain 'H' and resid 296 through 301 Processing helix chain 'H' and resid 309 through 329 removed outlier: 4.244A pdb=" N ARG H 313 " --> pdb=" O GLY H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 350 removed outlier: 3.586A pdb=" N LEU H 349 " --> pdb=" O LEU H 346 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY H 350 " --> pdb=" O ALA H 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 346 through 350' Processing helix chain 'H' and resid 355 through 367 Processing helix chain 'I' and resid 39 through 56 removed outlier: 3.502A pdb=" N TRP I 43 " --> pdb=" O SER I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 76 removed outlier: 3.720A pdb=" N GLU I 68 " --> pdb=" O ARG I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 93 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.939A pdb=" N HIS I 134 " --> pdb=" O ILE I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 144 removed outlier: 3.858A pdb=" N LYS I 144 " --> pdb=" O LYS I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE I 156 " --> pdb=" O PRO I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 171 Processing helix chain 'I' and resid 239 through 247 Processing helix chain 'I' and resid 248 through 266 Processing helix chain 'I' and resid 296 through 301 Processing helix chain 'I' and resid 309 through 329 removed outlier: 4.243A pdb=" N ARG I 313 " --> pdb=" O GLY I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 350 removed outlier: 3.588A pdb=" N LEU I 349 " --> pdb=" O LEU I 346 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY I 350 " --> pdb=" O ALA I 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 346 through 350' Processing helix chain 'I' and resid 355 through 367 Processing helix chain 'J' and resid 6 through 24 removed outlier: 4.033A pdb=" N VAL J 22 " --> pdb=" O SER J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 33 removed outlier: 3.691A pdb=" N ARG J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 45 Processing helix chain 'J' and resid 47 through 52 Processing helix chain 'J' and resid 53 through 55 No H-bonds generated for 'chain 'J' and resid 53 through 55' Processing helix chain 'J' and resid 75 through 90 Processing helix chain 'J' and resid 92 through 98 removed outlier: 3.753A pdb=" N GLN J 98 " --> pdb=" O SER J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 149 Processing helix chain 'J' and resid 153 through 165 Processing helix chain 'J' and resid 168 through 186 removed outlier: 3.604A pdb=" N HIS J 173 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG J 174 " --> pdb=" O ASP J 170 " (cutoff:3.500A) Proline residue: J 177 - end of helix removed outlier: 4.013A pdb=" N ASP J 186 " --> pdb=" O TYR J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 202 Processing helix chain 'J' and resid 209 through 228 removed outlier: 3.554A pdb=" N ALA J 228 " --> pdb=" O LEU J 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 24 removed outlier: 3.694A pdb=" N HIS L 9 " --> pdb=" O TYR L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 33 Processing helix chain 'L' and resid 45 through 51 Processing helix chain 'L' and resid 75 through 90 removed outlier: 4.089A pdb=" N VAL L 84 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.650A pdb=" N GLN L 98 " --> pdb=" O SER L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 149 Processing helix chain 'L' and resid 153 through 167 removed outlier: 3.588A pdb=" N GLN L 159 " --> pdb=" O ASP L 155 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN L 167 " --> pdb=" O LEU L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 186 removed outlier: 3.869A pdb=" N HIS L 173 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG L 174 " --> pdb=" O ASP L 170 " (cutoff:3.500A) Proline residue: L 177 - end of helix Processing helix chain 'L' and resid 191 through 205 removed outlier: 3.881A pdb=" N GLY L 203 " --> pdb=" O LEU L 199 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS L 204 " --> pdb=" O ALA L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 229 removed outlier: 3.944A pdb=" N VAL L 209 " --> pdb=" O THR L 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 44 Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.724A pdb=" N THR N 85 " --> pdb=" O LYS N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 130 Processing helix chain 'N' and resid 157 through 164 removed outlier: 3.785A pdb=" N GLU N 161 " --> pdb=" O ASP N 157 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU N 164 " --> pdb=" O ARG N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 248 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 57 removed outlier: 6.302A pdb=" N TYR A 63 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 108 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 removed outlier: 4.039A pdb=" N VAL A 171 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 40 through 42 removed outlier: 3.674A pdb=" N ILE C 29 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 56 " --> pdb=" O ARG C 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.559A pdb=" N LEU C 176 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C 293 " --> pdb=" O HIS C 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 219 through 224 Processing sheet with id=AA8, first strand: chain 'C' and resid 315 through 318 removed outlier: 3.515A pdb=" N ARG C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 27 through 30 removed outlier: 6.291A pdb=" N THR D 36 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE D 192 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 187 through 188 removed outlier: 6.164A pdb=" N SER D 227 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR D 14 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP D 5 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 283 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 336 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 27 through 30 removed outlier: 6.162A pdb=" N THR E 36 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 27 through 30 removed outlier: 6.162A pdb=" N THR E 36 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 59 through 62 Processing sheet with id=AB5, first strand: chain 'E' and resid 200 through 207 Processing sheet with id=AB6, first strand: chain 'F' and resid 27 through 30 removed outlier: 6.161A pdb=" N THR F 36 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 27 through 30 removed outlier: 6.161A pdb=" N THR F 36 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 59 through 62 Processing sheet with id=AB9, first strand: chain 'F' and resid 200 through 206 Processing sheet with id=AC1, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.160A pdb=" N THR G 36 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.160A pdb=" N THR G 36 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 59 through 62 Processing sheet with id=AC4, first strand: chain 'G' and resid 200 through 205 Processing sheet with id=AC5, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.160A pdb=" N THR H 36 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.160A pdb=" N THR H 36 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 59 through 62 Processing sheet with id=AC8, first strand: chain 'H' and resid 200 through 207 Processing sheet with id=AC9, first strand: chain 'I' and resid 27 through 30 removed outlier: 6.162A pdb=" N THR I 36 " --> pdb=" O THR I 193 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 27 through 30 removed outlier: 6.162A pdb=" N THR I 36 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY I 229 " --> pdb=" O LEU I 12 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 59 through 62 Processing sheet with id=AD3, first strand: chain 'N' and resid 150 through 152 removed outlier: 5.274A pdb=" N VAL N 150 " --> pdb=" O ARG N 7 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG N 7 " --> pdb=" O VAL N 150 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG N 152 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL N 112 " --> pdb=" O ASP N 64 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG N 62 " --> pdb=" O THR N 114 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR N 60 " --> pdb=" O ALA N 116 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP N 183 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N ARG N 65 " --> pdb=" O LEU N 181 " (cutoff:3.500A) removed outlier: 13.805A pdb=" N LEU N 181 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG N 213 " --> pdb=" O PRO N 204 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N SER N 215 " --> pdb=" O ASP N 202 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU N 200 " --> pdb=" O ARG N 217 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 12 through 13 Processing sheet with id=AD5, first strand: chain 'N' and resid 12 through 13 1333 hydrogen bonds defined for protein. 3720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 5.87 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6173 1.32 - 1.45: 8270 1.45 - 1.58: 15021 1.58 - 1.71: 268 1.71 - 1.84: 80 Bond restraints: 29812 Sorted by residual: bond pdb=" C1' C K 55 " pdb=" N1 C K 55 " ideal model delta sigma weight residual 1.480 1.567 -0.087 1.50e-02 4.44e+03 3.35e+01 bond pdb=" C LEU I 12 " pdb=" N PRO I 13 " ideal model delta sigma weight residual 1.329 1.388 -0.059 1.20e-02 6.94e+03 2.43e+01 bond pdb=" C GLN C 84 " pdb=" N PRO C 85 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.18e-02 7.18e+03 2.38e+01 bond pdb=" C ARG C 130 " pdb=" N PRO C 131 " ideal model delta sigma weight residual 1.331 1.390 -0.060 1.31e-02 5.83e+03 2.08e+01 bond pdb=" C ASP C 256 " pdb=" N PRO C 257 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.20e-02 6.94e+03 2.00e+01 ... (remaining 29807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.85: 41080 9.85 - 19.69: 39 19.69 - 29.54: 0 29.54 - 39.39: 0 39.39 - 49.23: 1 Bond angle restraints: 41120 Sorted by residual: angle pdb=" C HIS A 185 " pdb=" N PRO A 186 " pdb=" CD PRO A 186 " ideal model delta sigma weight residual 125.00 75.77 49.23 4.10e+00 5.95e-02 1.44e+02 angle pdb=" N GLY C 166 " pdb=" CA GLY C 166 " pdb=" C GLY C 166 " ideal model delta sigma weight residual 112.68 97.58 15.10 1.26e+00 6.30e-01 1.44e+02 angle pdb=" N TRP C 163 " pdb=" CA TRP C 163 " pdb=" C TRP C 163 " ideal model delta sigma weight residual 111.28 123.18 -11.90 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N ARG A 123 " pdb=" CA ARG A 123 " pdb=" C ARG A 123 " ideal model delta sigma weight residual 110.59 96.14 14.45 1.45e+00 4.76e-01 9.93e+01 angle pdb=" N ILE C 236 " pdb=" CA ILE C 236 " pdb=" C ILE C 236 " ideal model delta sigma weight residual 107.76 116.98 -9.22 1.01e+00 9.80e-01 8.33e+01 ... (remaining 41115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.17: 16770 32.17 - 64.34: 963 64.34 - 96.51: 52 96.51 - 128.68: 3 128.68 - 160.85: 3 Dihedral angle restraints: 17791 sinusoidal: 8136 harmonic: 9655 Sorted by residual: dihedral pdb=" O4' C K 55 " pdb=" C1' C K 55 " pdb=" N1 C K 55 " pdb=" C2 C K 55 " ideal model delta sinusoidal sigma weight residual 200.00 45.88 154.12 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" O4' U K 20 " pdb=" C1' U K 20 " pdb=" N1 U K 20 " pdb=" C2 U K 20 " ideal model delta sinusoidal sigma weight residual 200.00 82.12 117.88 1 1.50e+01 4.44e-03 6.26e+01 dihedral pdb=" N TYR A 164 " pdb=" C TYR A 164 " pdb=" CA TYR A 164 " pdb=" CB TYR A 164 " ideal model delta harmonic sigma weight residual 122.80 110.73 12.07 0 2.50e+00 1.60e-01 2.33e+01 ... (remaining 17788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4398 0.149 - 0.298: 234 0.298 - 0.448: 20 0.448 - 0.597: 2 0.597 - 0.746: 1 Chirality restraints: 4655 Sorted by residual: chirality pdb=" CG LEU N 138 " pdb=" CB LEU N 138 " pdb=" CD1 LEU N 138 " pdb=" CD2 LEU N 138 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CB THR D 193 " pdb=" CA THR D 193 " pdb=" OG1 THR D 193 " pdb=" CG2 THR D 193 " both_signs ideal model delta sigma weight residual False 2.55 1.99 0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C1' DA M 50 " pdb=" O4' DA M 50 " pdb=" C2' DA M 50 " pdb=" N9 DA M 50 " both_signs ideal model delta sigma weight residual False 2.42 1.93 0.49 2.00e-01 2.50e+01 6.01e+00 ... (remaining 4652 not shown) Planarity restraints: 4869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 185 " -0.156 5.00e-02 4.00e+02 2.33e-01 8.66e+01 pdb=" N PRO A 186 " 0.398 5.00e-02 4.00e+02 pdb=" CA PRO A 186 " -0.167 5.00e-02 4.00e+02 pdb=" CD PRO A 186 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 427 " 0.034 2.00e-02 2.50e+03 6.90e-02 4.76e+01 pdb=" CD GLU C 427 " -0.119 2.00e-02 2.50e+03 pdb=" OE1 GLU C 427 " 0.042 2.00e-02 2.50e+03 pdb=" OE2 GLU C 427 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 390 " 0.006 2.00e-02 2.50e+03 3.67e-02 3.37e+01 pdb=" CG TRP C 390 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP C 390 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP C 390 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 390 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP C 390 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 390 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 390 " -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 390 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP C 390 " 0.003 2.00e-02 2.50e+03 ... (remaining 4866 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 94 2.31 - 2.96: 14742 2.96 - 3.61: 43232 3.61 - 4.25: 69502 4.25 - 4.90: 116165 Nonbonded interactions: 243735 Sorted by model distance: nonbonded pdb=" NE2 GLN A 122 " pdb=" N1 A K 44 " model vdw 1.667 3.200 nonbonded pdb=" OE1 GLN A 122 " pdb=" C5 A K 44 " model vdw 1.818 3.260 nonbonded pdb=" O ASP A 169 " pdb=" O ARG A 184 " model vdw 1.858 3.040 nonbonded pdb=" O GLN J 98 " pdb=" NE2 GLN J 98 " model vdw 1.876 3.120 nonbonded pdb=" NH2 ARG A 184 " pdb=" OP1 C K 46 " model vdw 1.926 3.120 ... (remaining 243730 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 'E' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 198 or resid 227 through 247 or (re \ sid 248 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 through 269 or resid 279 through 367)) selection = (chain 'F' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 198 or resid 227 through 247 or (re \ sid 248 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 through 269 or resid 279 through 367)) selection = (chain 'G' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 198 or resid 227 through 247 or (re \ sid 248 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 through 269 or resid 279 through 367)) selection = (chain 'H' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 198 or resid 227 through 247 or (re \ sid 248 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 through 269 or resid 279 through 367)) selection = chain 'I' } ncs_group { reference = (chain 'J' and (resid 5 through 35 or resid 44 through 57 or resid 75 through 13 \ 5 or resid 137 through 215 or (resid 216 and (name N or name CA or name C or nam \ e O or name CB )) or resid 217 through 229)) selection = (chain 'L' and resid 5 through 229) } 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.690 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 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 : 0.012 0.151 29812 Z= 0.573 Angle : 1.365 49.234 41120 Z= 0.784 Chirality : 0.078 0.746 4655 Planarity : 0.008 0.233 4869 Dihedral : 17.115 160.852 11537 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 28.68 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.65 % Favored : 94.80 % Rotamer: Outliers : 5.48 % Allowed : 6.64 % Favored : 87.88 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.78 (0.12), residues: 3269 helix: -1.73 (0.11), residues: 1356 sheet: -2.28 (0.19), residues: 490 loop : -1.59 (0.14), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG A 113 TYR 0.085 0.004 TYR C 315 PHE 0.080 0.004 PHE E 226 TRP 0.079 0.006 TRP C 390 HIS 0.024 0.004 HIS H 216 Details of bonding type rmsd covalent geometry : bond 0.01249 (29812) covalent geometry : angle 1.36539 (41120) hydrogen bonds : bond 0.15781 ( 1357) hydrogen bonds : angle 8.57061 ( 3858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 730 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.1497 (mtt) cc_final: 0.0768 (mtm) REVERT: A 112 LYS cc_start: 0.3622 (OUTLIER) cc_final: 0.2391 (tttt) REVERT: C 51 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8114 (t) REVERT: C 106 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5857 (ptm-80) REVERT: C 118 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7702 (t0) REVERT: C 169 HIS cc_start: 0.6420 (OUTLIER) cc_final: 0.6189 (m90) REVERT: C 215 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8321 (pp) REVERT: C 336 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6769 (ttt180) REVERT: C 343 HIS cc_start: 0.6462 (OUTLIER) cc_final: 0.4987 (t-90) REVERT: C 357 ASN cc_start: 0.7696 (m-40) cc_final: 0.7479 (m110) REVERT: C 424 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8632 (mmmt) REVERT: C 434 GLU cc_start: 0.6339 (pp20) cc_final: 0.5744 (pp20) REVERT: C 522 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7296 (mtm180) REVERT: D 20 ASP cc_start: 0.8280 (m-30) cc_final: 0.8009 (m-30) REVERT: D 50 GLU cc_start: 0.7879 (tp30) cc_final: 0.7602 (tp30) REVERT: D 341 GLU cc_start: 0.5122 (OUTLIER) cc_final: 0.4919 (pp20) REVERT: D 354 ASP cc_start: 0.7225 (m-30) cc_final: 0.6917 (p0) REVERT: E 21 ASP cc_start: 0.8093 (t70) cc_final: 0.7543 (p0) REVERT: E 148 LYS cc_start: 0.8241 (mttp) cc_final: 0.7474 (mmmm) REVERT: E 266 THR cc_start: 0.9017 (t) cc_final: 0.8732 (p) REVERT: F 5 ASP cc_start: 0.8052 (p0) cc_final: 0.7834 (p0) REVERT: F 22 LEU cc_start: 0.8488 (mt) cc_final: 0.8253 (mt) REVERT: F 113 THR cc_start: 0.8759 (p) cc_final: 0.8519 (t) REVERT: F 119 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8313 (pp) REVERT: G 154 ASP cc_start: 0.7811 (t0) cc_final: 0.7357 (t0) REVERT: G 221 MET cc_start: 0.8833 (mtp) cc_final: 0.8281 (mtp) REVERT: H 155 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7498 (mtp180) REVERT: H 208 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: H 234 TYR cc_start: 0.8959 (t80) cc_final: 0.8624 (t80) REVERT: H 253 ARG cc_start: 0.7984 (ttt-90) cc_final: 0.6145 (mmt-90) REVERT: I 147 PRO cc_start: 0.7757 (Cg_endo) cc_final: 0.7482 (Cg_exo) REVERT: J 157 THR cc_start: 0.9367 (t) cc_final: 0.9031 (p) REVERT: J 211 ARG cc_start: 0.7214 (mmm160) cc_final: 0.6924 (mtp85) REVERT: L 8 GLN cc_start: 0.7226 (mt0) cc_final: 0.6751 (mt0) REVERT: L 18 SER cc_start: 0.7752 (t) cc_final: 0.7548 (p) REVERT: L 182 TYR cc_start: 0.8434 (t80) cc_final: 0.8230 (t80) REVERT: L 191 ASP cc_start: 0.8586 (t0) cc_final: 0.8305 (t0) REVERT: N 13 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8381 (pt0) REVERT: N 65 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7402 (ttp-170) REVERT: N 110 ASP cc_start: 0.6775 (t70) cc_final: 0.6373 (t70) REVERT: N 137 TYR cc_start: 0.8150 (p90) cc_final: 0.7901 (p90) REVERT: N 205 LEU cc_start: 0.8330 (mp) cc_final: 0.7900 (mp) REVERT: N 206 SER cc_start: 0.8069 (t) cc_final: 0.7487 (t) REVERT: N 244 THR cc_start: 0.8417 (m) cc_final: 0.8104 (p) outliers start: 146 outliers final: 48 residues processed: 835 average time/residue: 0.2546 time to fit residues: 308.8453 Evaluate side-chains 445 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 382 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 335 TRP Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 522 ARG Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 368 PHE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain L residue 197 ARG Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 18 HIS Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 231 VAL Chi-restraints excluded: chain N residue 242 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 HIS C 100 GLN ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 ASN D 245 ASN E 18 ASN E 89 GLN E 134 HIS E 195 HIS F 18 ASN F 89 GLN F 195 HIS F 216 HIS F 222 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS G 195 HIS ** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 ASN H 89 GLN ** H 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 HIS H 214 ASN H 225 GLN I 134 HIS L 145 GLN L 167 GLN L 173 HIS L 175 HIS L 208 HIS N 43 GLN ** N 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.165838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128088 restraints weight = 40569.089| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.85 r_work: 0.3291 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29812 Z= 0.162 Angle : 0.699 21.280 41120 Z= 0.369 Chirality : 0.044 0.302 4655 Planarity : 0.006 0.181 4869 Dihedral : 19.094 156.556 5689 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.81 % Favored : 96.97 % Rotamer: Outliers : 4.24 % Allowed : 12.16 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.21 (0.13), residues: 3269 helix: 0.01 (0.13), residues: 1367 sheet: -1.76 (0.20), residues: 480 loop : -1.15 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 432 TYR 0.020 0.002 TYR I 321 PHE 0.036 0.002 PHE C 379 TRP 0.022 0.002 TRP C 183 HIS 0.010 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00345 (29812) covalent geometry : angle 0.69889 (41120) hydrogen bonds : bond 0.05137 ( 1357) hydrogen bonds : angle 5.51350 ( 3858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 515 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.2308 (mtt) cc_final: 0.1699 (mtm) REVERT: C 24 ILE cc_start: 0.7755 (mp) cc_final: 0.7536 (pt) REVERT: C 97 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7394 (mtt180) REVERT: C 118 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7824 (t0) REVERT: C 129 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7420 (pp20) REVERT: C 169 HIS cc_start: 0.6520 (OUTLIER) cc_final: 0.6119 (m90) REVERT: C 343 HIS cc_start: 0.6562 (OUTLIER) cc_final: 0.5089 (t-90) REVERT: C 357 ASN cc_start: 0.7744 (m-40) cc_final: 0.7517 (m110) REVERT: C 406 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5248 (pm20) REVERT: C 434 GLU cc_start: 0.7112 (pp20) cc_final: 0.6779 (pp20) REVERT: C 438 LYS cc_start: 0.9018 (tttp) cc_final: 0.8559 (ttmt) REVERT: C 441 TRP cc_start: 0.8253 (t60) cc_final: 0.8020 (t-100) REVERT: C 445 ASN cc_start: 0.7367 (m110) cc_final: 0.6497 (t0) REVERT: D 20 ASP cc_start: 0.8199 (m-30) cc_final: 0.7914 (m-30) REVERT: D 173 MET cc_start: 0.6879 (mmm) cc_final: 0.6653 (mmm) REVERT: D 296 PHE cc_start: 0.9191 (m-10) cc_final: 0.8906 (m-10) REVERT: D 341 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.5757 (pp20) REVERT: D 354 ASP cc_start: 0.7654 (m-30) cc_final: 0.7360 (p0) REVERT: E 148 LYS cc_start: 0.8368 (mttp) cc_final: 0.8088 (mmmm) REVERT: E 266 THR cc_start: 0.9101 (t) cc_final: 0.8873 (p) REVERT: E 312 LEU cc_start: 0.7951 (tp) cc_final: 0.7708 (tp) REVERT: E 363 MET cc_start: 0.8215 (mmt) cc_final: 0.7529 (mmt) REVERT: F 75 GLU cc_start: 0.7876 (pp20) cc_final: 0.7381 (tt0) REVERT: F 97 LYS cc_start: 0.6926 (mptt) cc_final: 0.6391 (ttpt) REVERT: F 301 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7940 (tm-30) REVERT: G 43 TRP cc_start: 0.9285 (OUTLIER) cc_final: 0.8703 (t-100) REVERT: G 50 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7510 (tp30) REVERT: G 221 MET cc_start: 0.8525 (mtp) cc_final: 0.8306 (mtp) REVERT: G 227 SER cc_start: 0.9067 (t) cc_final: 0.8556 (m) REVERT: H 158 GLU cc_start: 0.8027 (tp30) cc_final: 0.7675 (pt0) REVERT: H 208 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: H 221 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8339 (ptp) REVERT: H 253 ARG cc_start: 0.8250 (ttt-90) cc_final: 0.6440 (mmt-90) REVERT: H 363 MET cc_start: 0.8910 (mmt) cc_final: 0.8169 (mmt) REVERT: I 250 GLN cc_start: 0.7907 (mm110) cc_final: 0.7505 (tp-100) REVERT: J 172 VAL cc_start: 0.9080 (t) cc_final: 0.8848 (p) REVERT: L 8 GLN cc_start: 0.7350 (mt0) cc_final: 0.6839 (mt0) REVERT: L 226 ARG cc_start: 0.7544 (mmt-90) cc_final: 0.7249 (mmt-90) REVERT: N 13 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8850 (pt0) REVERT: N 65 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7875 (ttp-170) REVERT: N 69 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8194 (ttm110) REVERT: N 83 GLU cc_start: 0.7943 (mp0) cc_final: 0.7660 (mp0) REVERT: N 110 ASP cc_start: 0.7195 (t70) cc_final: 0.6662 (t70) REVERT: N 206 SER cc_start: 0.8189 (t) cc_final: 0.7724 (p) REVERT: N 225 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7783 (mm-30) outliers start: 113 outliers final: 48 residues processed: 594 average time/residue: 0.2232 time to fit residues: 200.6411 Evaluate side-chains 434 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 373 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 221 MET Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 181 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 334 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 301 optimal weight: 0.0070 chunk 204 optimal weight: 1.9990 chunk 166 optimal weight: 0.0670 chunk 227 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS E 89 GLN F 49 HIS ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN H 18 ASN H 49 HIS H 134 HIS H 225 GLN H 273 ASN J 23 ASN J 91 GLN L 215 GLN L 218 HIS ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.164381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125976 restraints weight = 40388.628| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.85 r_work: 0.3276 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29812 Z= 0.137 Angle : 0.604 13.299 41120 Z= 0.317 Chirality : 0.041 0.183 4655 Planarity : 0.005 0.152 4869 Dihedral : 18.607 156.103 5591 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.57 % Rotamer: Outliers : 3.71 % Allowed : 14.56 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.47 (0.14), residues: 3269 helix: 0.76 (0.14), residues: 1375 sheet: -1.36 (0.21), residues: 482 loop : -0.91 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 324 TYR 0.017 0.002 TYR E 118 PHE 0.017 0.001 PHE I 231 TRP 0.014 0.001 TRP C 132 HIS 0.010 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00298 (29812) covalent geometry : angle 0.60377 (41120) hydrogen bonds : bond 0.04355 ( 1357) hydrogen bonds : angle 4.89956 ( 3858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 428 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.2070 (mtt) cc_final: 0.1650 (mtm) REVERT: C 24 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7574 (pt) REVERT: C 42 LEU cc_start: 0.7802 (pp) cc_final: 0.7330 (pp) REVERT: C 46 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8091 (t70) REVERT: C 76 THR cc_start: 0.7358 (OUTLIER) cc_final: 0.6992 (t) REVERT: C 97 ARG cc_start: 0.7536 (mtt180) cc_final: 0.7319 (mtt180) REVERT: C 118 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8007 (t0) REVERT: C 215 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8703 (pp) REVERT: C 434 GLU cc_start: 0.7327 (pp20) cc_final: 0.7112 (pp20) REVERT: C 438 LYS cc_start: 0.9105 (tttp) cc_final: 0.8588 (ttmt) REVERT: C 441 TRP cc_start: 0.8449 (t60) cc_final: 0.8211 (t-100) REVERT: C 445 ASN cc_start: 0.6929 (m110) cc_final: 0.6291 (t0) REVERT: C 478 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7418 (tp30) REVERT: C 497 MET cc_start: 0.7049 (mtp) cc_final: 0.6818 (mtp) REVERT: D 50 GLU cc_start: 0.8500 (tp30) cc_final: 0.8127 (tp30) REVERT: D 173 MET cc_start: 0.6825 (mmm) cc_final: 0.6599 (mmm) REVERT: D 234 TYR cc_start: 0.8802 (t80) cc_final: 0.8542 (t80) REVERT: D 341 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6236 (mt-10) REVERT: D 354 ASP cc_start: 0.8062 (m-30) cc_final: 0.7623 (p0) REVERT: E 124 ILE cc_start: 0.8238 (tt) cc_final: 0.7940 (mt) REVERT: E 148 LYS cc_start: 0.8246 (mttp) cc_final: 0.7934 (mmmm) REVERT: E 213 GLU cc_start: 0.7002 (tt0) cc_final: 0.6790 (tp30) REVERT: E 221 MET cc_start: 0.7272 (mtp) cc_final: 0.6723 (mtp) REVERT: E 222 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7435 (m110) REVERT: E 266 THR cc_start: 0.9214 (t) cc_final: 0.9013 (p) REVERT: E 312 LEU cc_start: 0.8061 (tp) cc_final: 0.7833 (tp) REVERT: E 316 GLN cc_start: 0.8129 (mt0) cc_final: 0.7702 (mt0) REVERT: E 363 MET cc_start: 0.8260 (mmt) cc_final: 0.7711 (mmt) REVERT: F 74 ARG cc_start: 0.7968 (ttm170) cc_final: 0.7458 (mtp180) REVERT: F 97 LYS cc_start: 0.7114 (mptt) cc_final: 0.6494 (ttpt) REVERT: F 125 ASP cc_start: 0.7635 (t0) cc_final: 0.7257 (t0) REVERT: F 135 ARG cc_start: 0.7598 (ttt180) cc_final: 0.7327 (ttt-90) REVERT: F 208 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7938 (m-30) REVERT: F 258 GLU cc_start: 0.8758 (tp30) cc_final: 0.8266 (mm-30) REVERT: F 278 MET cc_start: 0.9030 (mmm) cc_final: 0.8438 (mmt) REVERT: F 301 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8107 (tm-30) REVERT: G 43 TRP cc_start: 0.9322 (OUTLIER) cc_final: 0.8909 (t-100) REVERT: G 91 VAL cc_start: 0.8413 (t) cc_final: 0.7808 (m) REVERT: G 140 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7871 (mmtm) REVERT: G 173 MET cc_start: 0.8919 (ttt) cc_final: 0.8603 (ttt) REVERT: G 225 GLN cc_start: 0.8742 (pm20) cc_final: 0.8476 (mp10) REVERT: G 227 SER cc_start: 0.8995 (t) cc_final: 0.8556 (m) REVERT: H 119 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9106 (pp) REVERT: H 158 GLU cc_start: 0.8261 (tp30) cc_final: 0.7671 (pt0) REVERT: H 208 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: H 221 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8278 (ptp) REVERT: H 253 ARG cc_start: 0.8526 (ttt-90) cc_final: 0.6396 (mmt-90) REVERT: H 363 MET cc_start: 0.9119 (mmt) cc_final: 0.8538 (mmt) REVERT: I 188 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8035 (t80) REVERT: I 193 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8715 (p) REVERT: I 250 GLN cc_start: 0.8083 (mm110) cc_final: 0.7621 (tp-100) REVERT: J 172 VAL cc_start: 0.9072 (t) cc_final: 0.8796 (p) REVERT: J 207 ARG cc_start: 0.6683 (mtp85) cc_final: 0.6401 (mtp-110) REVERT: L 8 GLN cc_start: 0.7336 (mt0) cc_final: 0.6814 (mt0) REVERT: L 88 MET cc_start: 0.9015 (mtp) cc_final: 0.8732 (ttm) REVERT: L 182 TYR cc_start: 0.8627 (t80) cc_final: 0.8120 (t80) REVERT: L 191 ASP cc_start: 0.8685 (t0) cc_final: 0.8307 (t0) REVERT: N 110 ASP cc_start: 0.7547 (t70) cc_final: 0.7158 (t0) REVERT: N 225 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7678 (mm-30) outliers start: 99 outliers final: 47 residues processed: 499 average time/residue: 0.2112 time to fit residues: 162.8440 Evaluate side-chains 419 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 357 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 221 MET Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 215 SER Chi-restraints excluded: chain N residue 219 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 48 optimal weight: 2.9990 chunk 265 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 12 optimal weight: 30.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN C 363 GLN ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN H 225 GLN I 195 HIS J 9 HIS J 173 HIS ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.155579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115904 restraints weight = 40034.252| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.95 r_work: 0.3125 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 29812 Z= 0.224 Angle : 0.653 10.181 41120 Z= 0.345 Chirality : 0.044 0.208 4655 Planarity : 0.006 0.134 4869 Dihedral : 18.422 157.758 5558 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.06 % Favored : 96.79 % Rotamer: Outliers : 4.35 % Allowed : 15.68 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.25 (0.14), residues: 3269 helix: 0.96 (0.14), residues: 1364 sheet: -1.32 (0.21), residues: 460 loop : -0.78 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 289 TYR 0.019 0.002 TYR E 118 PHE 0.017 0.002 PHE C 379 TRP 0.022 0.002 TRP C 390 HIS 0.008 0.002 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00521 (29812) covalent geometry : angle 0.65321 (41120) hydrogen bonds : bond 0.04568 ( 1357) hydrogen bonds : angle 4.86463 ( 3858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 374 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.2186 (mtt) cc_final: 0.1665 (mtm) REVERT: C 21 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7956 (t0) REVERT: C 24 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7709 (pt) REVERT: C 42 LEU cc_start: 0.8194 (pp) cc_final: 0.7949 (pp) REVERT: C 56 ASP cc_start: 0.6541 (t0) cc_final: 0.6300 (t70) REVERT: C 200 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.4431 (pmt-80) REVERT: C 215 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8609 (pp) REVERT: C 357 ASN cc_start: 0.8042 (m-40) cc_final: 0.7687 (m-40) REVERT: C 438 LYS cc_start: 0.9086 (tttp) cc_final: 0.8635 (ttmt) REVERT: C 441 TRP cc_start: 0.8511 (t60) cc_final: 0.8259 (t-100) REVERT: C 445 ASN cc_start: 0.7314 (m110) cc_final: 0.6392 (t0) REVERT: C 478 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: C 497 MET cc_start: 0.7084 (mtp) cc_final: 0.6755 (mtp) REVERT: D 7 HIS cc_start: 0.9142 (OUTLIER) cc_final: 0.8854 (m-70) REVERT: D 50 GLU cc_start: 0.8511 (tp30) cc_final: 0.8077 (tp30) REVERT: D 260 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9277 (mp) REVERT: D 317 GLU cc_start: 0.7719 (tp30) cc_final: 0.7465 (mm-30) REVERT: D 354 ASP cc_start: 0.8327 (m-30) cc_final: 0.7942 (p0) REVERT: E 124 ILE cc_start: 0.8371 (tt) cc_final: 0.8106 (mt) REVERT: E 148 LYS cc_start: 0.8339 (mttp) cc_final: 0.8030 (mmmm) REVERT: E 221 MET cc_start: 0.7187 (mtp) cc_final: 0.6653 (mtp) REVERT: E 222 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7752 (m110) REVERT: E 316 GLN cc_start: 0.8276 (mt0) cc_final: 0.7856 (mt0) REVERT: F 97 LYS cc_start: 0.7402 (mptt) cc_final: 0.6714 (ttpt) REVERT: F 208 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: F 258 GLU cc_start: 0.8792 (tp30) cc_final: 0.8316 (mm-30) REVERT: F 278 MET cc_start: 0.9187 (mmm) cc_final: 0.8601 (mmt) REVERT: G 7 HIS cc_start: 0.9023 (OUTLIER) cc_final: 0.8678 (m-70) REVERT: G 43 TRP cc_start: 0.9460 (OUTLIER) cc_final: 0.8894 (t-100) REVERT: G 173 MET cc_start: 0.9037 (ttt) cc_final: 0.8657 (ttt) REVERT: G 320 ASN cc_start: 0.8913 (t0) cc_final: 0.8706 (t0) REVERT: H 119 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9244 (pp) REVERT: H 158 GLU cc_start: 0.8365 (tp30) cc_final: 0.7663 (pt0) REVERT: H 208 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: H 253 ARG cc_start: 0.8659 (ttt-90) cc_final: 0.6475 (mmt-90) REVERT: H 341 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: H 363 MET cc_start: 0.9256 (mmt) cc_final: 0.8353 (mmt) REVERT: I 193 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8764 (p) REVERT: I 250 GLN cc_start: 0.8265 (mm110) cc_final: 0.7972 (tp40) REVERT: J 172 VAL cc_start: 0.9192 (t) cc_final: 0.8871 (p) REVERT: J 186 ASP cc_start: 0.8469 (p0) cc_final: 0.8222 (p0) REVERT: L 8 GLN cc_start: 0.7735 (mt0) cc_final: 0.7397 (mt0) REVERT: L 88 MET cc_start: 0.9007 (mtp) cc_final: 0.8793 (ttm) REVERT: L 170 ASP cc_start: 0.8515 (m-30) cc_final: 0.8265 (m-30) REVERT: L 222 GLU cc_start: 0.8563 (tp30) cc_final: 0.8334 (tp30) REVERT: N 97 LYS cc_start: 0.7935 (tttt) cc_final: 0.7534 (tmtt) REVERT: N 110 ASP cc_start: 0.7831 (t70) cc_final: 0.7178 (t0) REVERT: N 206 SER cc_start: 0.8571 (t) cc_final: 0.8146 (p) outliers start: 116 outliers final: 60 residues processed: 461 average time/residue: 0.1939 time to fit residues: 140.8289 Evaluate side-chains 400 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 325 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 286 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 316 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN D 216 HIS D 225 GLN D 236 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN H 18 ASN H 225 GLN J 23 ASN ** J 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.155020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114782 restraints weight = 39996.895| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.91 r_work: 0.3154 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29812 Z= 0.191 Angle : 0.615 10.136 41120 Z= 0.325 Chirality : 0.042 0.202 4655 Planarity : 0.005 0.057 4869 Dihedral : 18.369 158.527 5550 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.24 % Favored : 96.64 % Rotamer: Outliers : 4.58 % Allowed : 16.74 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.14 (0.14), residues: 3269 helix: 1.06 (0.14), residues: 1376 sheet: -1.24 (0.22), residues: 449 loop : -0.77 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 211 TYR 0.021 0.002 TYR F 14 PHE 0.017 0.002 PHE L 81 TRP 0.017 0.001 TRP C 390 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00442 (29812) covalent geometry : angle 0.61507 (41120) hydrogen bonds : bond 0.04315 ( 1357) hydrogen bonds : angle 4.78519 ( 3858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 350 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 22 VAL cc_start: 0.8324 (t) cc_final: 0.8088 (p) REVERT: C 24 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7703 (pt) REVERT: C 76 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7457 (t) REVERT: C 200 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.4448 (pmt-80) REVERT: C 215 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8633 (pp) REVERT: C 357 ASN cc_start: 0.7849 (m-40) cc_final: 0.7504 (m-40) REVERT: C 438 LYS cc_start: 0.9072 (tttp) cc_final: 0.8653 (ttmt) REVERT: C 445 ASN cc_start: 0.7318 (m110) cc_final: 0.6614 (t0) REVERT: C 478 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7243 (tp30) REVERT: C 497 MET cc_start: 0.7148 (mtp) cc_final: 0.6848 (mtp) REVERT: C 524 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7374 (ptm-80) REVERT: D 7 HIS cc_start: 0.9066 (OUTLIER) cc_final: 0.8718 (m-70) REVERT: D 50 GLU cc_start: 0.8451 (tp30) cc_final: 0.8191 (tp30) REVERT: D 54 ARG cc_start: 0.7314 (mtp-110) cc_final: 0.6967 (mtp85) REVERT: D 258 GLU cc_start: 0.8669 (tp30) cc_final: 0.8352 (tp30) REVERT: D 260 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9247 (mp) REVERT: D 278 MET cc_start: 0.9052 (mmm) cc_final: 0.8791 (mmp) REVERT: D 329 TRP cc_start: 0.8370 (m-90) cc_final: 0.8089 (m-90) REVERT: E 148 LYS cc_start: 0.8400 (mttp) cc_final: 0.8108 (mmmm) REVERT: E 188 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: E 222 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7751 (m110) REVERT: E 316 GLN cc_start: 0.8226 (mt0) cc_final: 0.7836 (mt0) REVERT: F 97 LYS cc_start: 0.7487 (mptt) cc_final: 0.6791 (ttpt) REVERT: F 208 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8037 (m-30) REVERT: F 278 MET cc_start: 0.9212 (mmm) cc_final: 0.8599 (mmt) REVERT: F 344 THR cc_start: 0.8416 (m) cc_final: 0.7960 (p) REVERT: G 7 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8701 (m-70) REVERT: G 43 TRP cc_start: 0.9422 (OUTLIER) cc_final: 0.9044 (t-100) REVERT: G 154 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7452 (t0) REVERT: G 188 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8762 (t80) REVERT: H 7 HIS cc_start: 0.9332 (OUTLIER) cc_final: 0.9031 (m90) REVERT: H 119 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9215 (pp) REVERT: H 208 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: H 253 ARG cc_start: 0.8695 (ttt-90) cc_final: 0.6515 (mmt-90) REVERT: H 363 MET cc_start: 0.9281 (mmt) cc_final: 0.8199 (mmt) REVERT: I 119 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7922 (pp) REVERT: I 188 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7680 (t80) REVERT: I 193 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8791 (p) REVERT: I 289 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.7144 (ptm160) REVERT: I 316 GLN cc_start: 0.8460 (tp40) cc_final: 0.8177 (tp-100) REVERT: I 342 ASN cc_start: 0.5777 (t0) cc_final: 0.5029 (m-40) REVERT: J 172 VAL cc_start: 0.9091 (t) cc_final: 0.8829 (p) REVERT: J 186 ASP cc_start: 0.8330 (p0) cc_final: 0.8111 (p0) REVERT: L 8 GLN cc_start: 0.7780 (mt0) cc_final: 0.7518 (mt0) REVERT: L 88 MET cc_start: 0.8978 (mtp) cc_final: 0.8751 (ttm) REVERT: L 167 GLN cc_start: 0.8927 (mm110) cc_final: 0.8712 (mm110) REVERT: L 170 ASP cc_start: 0.8642 (m-30) cc_final: 0.8383 (m-30) REVERT: L 227 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7278 (mp10) REVERT: N 71 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8859 (t) REVERT: N 97 LYS cc_start: 0.8021 (tttt) cc_final: 0.7821 (tmtt) REVERT: N 110 ASP cc_start: 0.7789 (t70) cc_final: 0.7413 (t0) REVERT: N 127 ASP cc_start: 0.8350 (t0) cc_final: 0.8000 (m-30) REVERT: N 174 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7616 (mm-30) outliers start: 122 outliers final: 65 residues processed: 438 average time/residue: 0.2068 time to fit residues: 141.8770 Evaluate side-chains 400 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 311 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 524 ARG Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 104 LYS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain L residue 227 GLN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 53 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 260 optimal weight: 0.8980 chunk 337 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN E 18 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 HIS J 23 ASN J 175 HIS L 98 GLN L 153 ASN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.157802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118209 restraints weight = 39840.147| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.88 r_work: 0.3209 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29812 Z= 0.129 Angle : 0.571 10.097 41120 Z= 0.300 Chirality : 0.040 0.184 4655 Planarity : 0.005 0.057 4869 Dihedral : 18.278 159.663 5547 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.66 % Favored : 97.22 % Rotamer: Outliers : 3.86 % Allowed : 17.75 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 0.12 (0.14), residues: 3269 helix: 1.34 (0.14), residues: 1365 sheet: -1.07 (0.22), residues: 463 loop : -0.69 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 211 TYR 0.016 0.001 TYR N 137 PHE 0.013 0.001 PHE G 231 TRP 0.014 0.001 TRP C 132 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00286 (29812) covalent geometry : angle 0.57142 (41120) hydrogen bonds : bond 0.03950 ( 1357) hydrogen bonds : angle 4.58164 ( 3858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 366 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: -0.1749 (OUTLIER) cc_final: -0.2273 (tp) REVERT: C 22 VAL cc_start: 0.8282 (t) cc_final: 0.8068 (p) REVERT: C 24 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7662 (pt) REVERT: C 45 ARG cc_start: 0.7135 (ttt-90) cc_final: 0.6486 (ttp80) REVERT: C 76 THR cc_start: 0.7601 (OUTLIER) cc_final: 0.7262 (t) REVERT: C 215 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8668 (pp) REVERT: C 320 GLU cc_start: 0.6706 (mp0) cc_final: 0.6354 (mp0) REVERT: C 357 ASN cc_start: 0.7817 (m-40) cc_final: 0.7477 (m-40) REVERT: C 438 LYS cc_start: 0.9008 (tttp) cc_final: 0.8642 (ttmt) REVERT: C 445 ASN cc_start: 0.7152 (m110) cc_final: 0.6537 (t0) REVERT: C 478 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7309 (tp30) REVERT: C 497 MET cc_start: 0.7132 (mtp) cc_final: 0.6851 (mtp) REVERT: C 524 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7403 (ptm-80) REVERT: D 7 HIS cc_start: 0.9082 (OUTLIER) cc_final: 0.8750 (m-70) REVERT: D 50 GLU cc_start: 0.8491 (tp30) cc_final: 0.8088 (tp30) REVERT: D 54 ARG cc_start: 0.7344 (mtp-110) cc_final: 0.7049 (mtp85) REVERT: D 278 MET cc_start: 0.9053 (mmm) cc_final: 0.8730 (mmm) REVERT: D 289 ARG cc_start: 0.8560 (mtp85) cc_final: 0.8330 (mtp85) REVERT: E 124 ILE cc_start: 0.8331 (tt) cc_final: 0.7934 (mt) REVERT: E 148 LYS cc_start: 0.8242 (mttp) cc_final: 0.7865 (mmmm) REVERT: E 188 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: E 221 MET cc_start: 0.6919 (mtp) cc_final: 0.6598 (mtp) REVERT: E 324 ARG cc_start: 0.8220 (mtm180) cc_final: 0.7964 (mtm180) REVERT: F 97 LYS cc_start: 0.7679 (mptt) cc_final: 0.6868 (ttpt) REVERT: F 208 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: F 278 MET cc_start: 0.9218 (mmm) cc_final: 0.8571 (mmt) REVERT: F 344 THR cc_start: 0.8465 (m) cc_final: 0.8009 (p) REVERT: G 7 HIS cc_start: 0.9045 (OUTLIER) cc_final: 0.8741 (m-70) REVERT: G 43 TRP cc_start: 0.9411 (OUTLIER) cc_final: 0.9049 (t-100) REVERT: G 154 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7510 (t0) REVERT: G 173 MET cc_start: 0.8990 (ttt) cc_final: 0.8644 (ttt) REVERT: H 7 HIS cc_start: 0.9329 (OUTLIER) cc_final: 0.8840 (m-70) REVERT: H 119 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9176 (pp) REVERT: H 208 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: H 253 ARG cc_start: 0.8648 (ttt-90) cc_final: 0.6504 (mmt-90) REVERT: I 119 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7954 (pp) REVERT: I 188 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7780 (t80) REVERT: I 193 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8822 (p) REVERT: I 289 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.7202 (ptm160) REVERT: I 342 ASN cc_start: 0.5690 (t0) cc_final: 0.4969 (m-40) REVERT: J 172 VAL cc_start: 0.9006 (t) cc_final: 0.8739 (p) REVERT: L 8 GLN cc_start: 0.7741 (mt0) cc_final: 0.7472 (mt0) REVERT: L 88 MET cc_start: 0.9000 (mtp) cc_final: 0.8771 (ttm) REVERT: L 170 ASP cc_start: 0.8692 (m-30) cc_final: 0.8377 (m-30) REVERT: L 227 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: N 62 ARG cc_start: 0.8960 (ptt180) cc_final: 0.8657 (ttp80) REVERT: N 97 LYS cc_start: 0.8102 (tttt) cc_final: 0.7738 (tptm) REVERT: N 110 ASP cc_start: 0.7720 (t70) cc_final: 0.7312 (t0) REVERT: N 127 ASP cc_start: 0.8381 (t0) cc_final: 0.8052 (m-30) REVERT: N 164 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7402 (pt0) REVERT: N 174 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7589 (mm-30) outliers start: 103 outliers final: 54 residues processed: 444 average time/residue: 0.2083 time to fit residues: 142.2684 Evaluate side-chains 398 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 324 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 524 ARG Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain L residue 153 ASN Chi-restraints excluded: chain L residue 227 GLN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 66 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 339 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 276 optimal weight: 7.9990 chunk 309 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN E 342 ASN F 89 GLN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN I 89 GLN J 23 ASN J 175 HIS L 98 GLN L 153 ASN ** N 43 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 = 0.3846 r_free = 0.3846 target = 0.155333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115117 restraints weight = 39881.305| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.90 r_work: 0.3083 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29812 Z= 0.219 Angle : 0.627 10.267 41120 Z= 0.330 Chirality : 0.043 0.316 4655 Planarity : 0.005 0.068 4869 Dihedral : 18.182 160.108 5543 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.33 % Favored : 96.54 % Rotamer: Outliers : 4.50 % Allowed : 17.82 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 0.02 (0.14), residues: 3269 helix: 1.24 (0.14), residues: 1376 sheet: -1.05 (0.22), residues: 449 loop : -0.79 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 405 TYR 0.019 0.002 TYR N 137 PHE 0.016 0.002 PHE C 20 TRP 0.025 0.001 TRP C 132 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00512 (29812) covalent geometry : angle 0.62707 (41120) hydrogen bonds : bond 0.04339 ( 1357) hydrogen bonds : angle 4.68143 ( 3858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 323 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: -0.1501 (OUTLIER) cc_final: -0.2153 (tp) REVERT: C 22 VAL cc_start: 0.8223 (t) cc_final: 0.8022 (p) REVERT: C 24 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7678 (pt) REVERT: C 45 ARG cc_start: 0.7030 (ttt-90) cc_final: 0.6345 (ttp80) REVERT: C 76 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7805 (t) REVERT: C 200 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.3578 (pmt-80) REVERT: C 215 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8675 (pp) REVERT: C 357 ASN cc_start: 0.7969 (m-40) cc_final: 0.7652 (m-40) REVERT: C 434 GLU cc_start: 0.6886 (pp20) cc_final: 0.6663 (pp20) REVERT: C 438 LYS cc_start: 0.9037 (tttp) cc_final: 0.8651 (ttmt) REVERT: C 445 ASN cc_start: 0.7352 (m110) cc_final: 0.6573 (t0) REVERT: C 478 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: C 497 MET cc_start: 0.7109 (mtp) cc_final: 0.6812 (mtp) REVERT: C 524 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7380 (ptm-80) REVERT: D 7 HIS cc_start: 0.9155 (OUTLIER) cc_final: 0.8923 (m-70) REVERT: D 50 GLU cc_start: 0.8573 (tp30) cc_final: 0.8215 (tp30) REVERT: D 54 ARG cc_start: 0.7627 (mtp-110) cc_final: 0.7209 (mtp-110) REVERT: D 278 MET cc_start: 0.9020 (mmm) cc_final: 0.8652 (mmm) REVERT: E 148 LYS cc_start: 0.8359 (mttp) cc_final: 0.7999 (mmmm) REVERT: F 208 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: F 278 MET cc_start: 0.9174 (mmm) cc_final: 0.8511 (mmt) REVERT: F 344 THR cc_start: 0.8571 (m) cc_final: 0.8166 (p) REVERT: G 7 HIS cc_start: 0.9033 (OUTLIER) cc_final: 0.8671 (m-70) REVERT: G 43 TRP cc_start: 0.9411 (OUTLIER) cc_final: 0.9078 (t-100) REVERT: G 154 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7484 (t0) REVERT: H 7 HIS cc_start: 0.9343 (OUTLIER) cc_final: 0.8852 (m-70) REVERT: H 119 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9206 (pp) REVERT: H 174 LEU cc_start: 0.8459 (tp) cc_final: 0.8173 (tp) REVERT: H 208 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: H 253 ARG cc_start: 0.8716 (ttt-90) cc_final: 0.6532 (mmt-90) REVERT: H 363 MET cc_start: 0.9262 (mmt) cc_final: 0.8898 (mmt) REVERT: I 119 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7967 (pp) REVERT: I 193 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8776 (p) REVERT: I 289 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8466 (ptm160) REVERT: I 319 ASN cc_start: 0.8900 (t0) cc_final: 0.8482 (t0) REVERT: I 342 ASN cc_start: 0.5864 (t0) cc_final: 0.5383 (m-40) REVERT: J 172 VAL cc_start: 0.9071 (t) cc_final: 0.8824 (p) REVERT: L 8 GLN cc_start: 0.7876 (mt0) cc_final: 0.7624 (mt0) REVERT: L 170 ASP cc_start: 0.8701 (m-30) cc_final: 0.8361 (m-30) REVERT: L 227 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: N 110 ASP cc_start: 0.7852 (t70) cc_final: 0.7473 (t0) REVERT: N 127 ASP cc_start: 0.8531 (t0) cc_final: 0.8170 (m-30) REVERT: N 164 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7487 (pt0) REVERT: N 174 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7553 (mm-30) outliers start: 120 outliers final: 82 residues processed: 415 average time/residue: 0.2066 time to fit residues: 133.0133 Evaluate side-chains 401 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 300 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 524 ARG Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 225 GLN Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain L residue 153 ASN Chi-restraints excluded: chain L residue 227 GLN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 202 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 249 optimal weight: 0.0270 chunk 6 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN E 342 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN J 175 HIS L 98 GLN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116009 restraints weight = 39707.089| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.82 r_work: 0.3163 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29812 Z= 0.164 Angle : 0.600 12.079 41120 Z= 0.315 Chirality : 0.041 0.194 4655 Planarity : 0.005 0.060 4869 Dihedral : 18.171 160.452 5543 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 4.24 % Allowed : 18.57 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 0.09 (0.14), residues: 3269 helix: 1.32 (0.14), residues: 1371 sheet: -1.02 (0.22), residues: 458 loop : -0.75 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 98 TYR 0.019 0.002 TYR F 14 PHE 0.015 0.002 PHE C 20 TRP 0.020 0.001 TRP C 132 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00378 (29812) covalent geometry : angle 0.60026 (41120) hydrogen bonds : bond 0.04121 ( 1357) hydrogen bonds : angle 4.62177 ( 3858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 320 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7666 (pt) REVERT: C 42 LEU cc_start: 0.8242 (pp) cc_final: 0.7949 (pp) REVERT: C 76 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7573 (t) REVERT: C 200 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.4260 (pmt-80) REVERT: C 215 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8651 (pp) REVERT: C 357 ASN cc_start: 0.7919 (m-40) cc_final: 0.7546 (m-40) REVERT: C 421 LEU cc_start: 0.8498 (mt) cc_final: 0.8265 (mt) REVERT: C 434 GLU cc_start: 0.6801 (pp20) cc_final: 0.6596 (pp20) REVERT: C 438 LYS cc_start: 0.9004 (tttp) cc_final: 0.8630 (ttmt) REVERT: C 445 ASN cc_start: 0.7310 (m110) cc_final: 0.6544 (t0) REVERT: C 478 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7199 (tp30) REVERT: C 497 MET cc_start: 0.7146 (mtp) cc_final: 0.6891 (mtp) REVERT: C 524 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7404 (ptm-80) REVERT: D 7 HIS cc_start: 0.9134 (OUTLIER) cc_final: 0.8900 (m-70) REVERT: D 50 GLU cc_start: 0.8571 (tp30) cc_final: 0.8174 (tp30) REVERT: D 54 ARG cc_start: 0.7580 (mtp-110) cc_final: 0.7156 (mtp-110) REVERT: D 233 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8631 (mtp85) REVERT: D 278 MET cc_start: 0.8961 (mmm) cc_final: 0.8581 (mmm) REVERT: E 124 ILE cc_start: 0.8380 (tt) cc_final: 0.7994 (mt) REVERT: E 148 LYS cc_start: 0.8399 (mttp) cc_final: 0.8036 (mmmm) REVERT: F 208 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8125 (m-30) REVERT: F 278 MET cc_start: 0.9186 (mmm) cc_final: 0.8559 (mmt) REVERT: F 344 THR cc_start: 0.8544 (m) cc_final: 0.8148 (p) REVERT: G 7 HIS cc_start: 0.9053 (OUTLIER) cc_final: 0.8685 (m-70) REVERT: G 43 TRP cc_start: 0.9434 (OUTLIER) cc_final: 0.9131 (t-100) REVERT: G 154 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7458 (t0) REVERT: G 173 MET cc_start: 0.9014 (ttt) cc_final: 0.8666 (ttt) REVERT: H 7 HIS cc_start: 0.9346 (OUTLIER) cc_final: 0.8772 (m-70) REVERT: H 119 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9174 (pp) REVERT: H 174 LEU cc_start: 0.8441 (tp) cc_final: 0.8150 (tp) REVERT: H 208 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.7772 (m-30) REVERT: H 221 MET cc_start: 0.8740 (ptm) cc_final: 0.8500 (ptp) REVERT: H 253 ARG cc_start: 0.8716 (ttt-90) cc_final: 0.6502 (mmt-90) REVERT: H 363 MET cc_start: 0.9285 (mmt) cc_final: 0.8918 (mmt) REVERT: I 119 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8023 (pp) REVERT: I 188 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7705 (t80) REVERT: I 193 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8835 (p) REVERT: I 289 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8285 (ptm160) REVERT: I 319 ASN cc_start: 0.8844 (t0) cc_final: 0.8490 (t0) REVERT: I 342 ASN cc_start: 0.5481 (t0) cc_final: 0.5268 (m-40) REVERT: J 172 VAL cc_start: 0.9014 (t) cc_final: 0.8785 (p) REVERT: L 8 GLN cc_start: 0.7770 (mt0) cc_final: 0.7500 (mt0) REVERT: L 170 ASP cc_start: 0.8691 (m-30) cc_final: 0.8333 (m-30) REVERT: L 227 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: N 110 ASP cc_start: 0.7817 (t70) cc_final: 0.7421 (t0) REVERT: N 127 ASP cc_start: 0.8574 (t0) cc_final: 0.8194 (m-30) REVERT: N 164 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7466 (pt0) REVERT: N 174 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7505 (mm-30) outliers start: 113 outliers final: 75 residues processed: 406 average time/residue: 0.2086 time to fit residues: 131.5606 Evaluate side-chains 395 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 300 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 524 ARG Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain L residue 227 GLN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 32 optimal weight: 7.9990 chunk 276 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 282 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 116 optimal weight: 0.0770 chunk 179 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 218 optimal weight: 0.9990 chunk 294 optimal weight: 7.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN J 91 GLN L 98 GLN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.156413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115552 restraints weight = 39869.906| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.82 r_work: 0.3128 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29812 Z= 0.166 Angle : 0.600 14.253 41120 Z= 0.313 Chirality : 0.041 0.194 4655 Planarity : 0.005 0.061 4869 Dihedral : 18.128 160.901 5543 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 4.32 % Allowed : 18.65 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 0.11 (0.14), residues: 3269 helix: 1.35 (0.14), residues: 1371 sheet: -0.97 (0.22), residues: 455 loop : -0.77 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 98 TYR 0.019 0.002 TYR N 137 PHE 0.014 0.002 PHE C 20 TRP 0.017 0.001 TRP C 132 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00383 (29812) covalent geometry : angle 0.59959 (41120) hydrogen bonds : bond 0.04085 ( 1357) hydrogen bonds : angle 4.59002 ( 3858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 314 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7593 (pt) REVERT: C 42 LEU cc_start: 0.8246 (pp) cc_final: 0.7980 (pp) REVERT: C 76 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7694 (t) REVERT: C 200 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.4350 (pmt-80) REVERT: C 215 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8672 (pp) REVERT: C 357 ASN cc_start: 0.7901 (m-40) cc_final: 0.7505 (m-40) REVERT: C 421 LEU cc_start: 0.8524 (mt) cc_final: 0.8294 (mt) REVERT: C 434 GLU cc_start: 0.6831 (pp20) cc_final: 0.6560 (pp20) REVERT: C 438 LYS cc_start: 0.9009 (tttp) cc_final: 0.8643 (ttmt) REVERT: C 445 ASN cc_start: 0.7296 (m110) cc_final: 0.6557 (t0) REVERT: C 478 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: C 497 MET cc_start: 0.7138 (mtp) cc_final: 0.6888 (mtp) REVERT: C 524 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7391 (ptm-80) REVERT: D 7 HIS cc_start: 0.9152 (OUTLIER) cc_final: 0.8908 (m-70) REVERT: D 50 GLU cc_start: 0.8566 (tp30) cc_final: 0.8153 (tp30) REVERT: D 54 ARG cc_start: 0.7674 (mtp-110) cc_final: 0.7228 (mtp-110) REVERT: D 233 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8691 (mtp85) REVERT: D 278 MET cc_start: 0.8957 (mmm) cc_final: 0.8558 (mmm) REVERT: E 124 ILE cc_start: 0.8392 (tt) cc_final: 0.8016 (mt) REVERT: E 148 LYS cc_start: 0.8399 (mttp) cc_final: 0.8042 (mmmm) REVERT: F 208 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8106 (m-30) REVERT: F 278 MET cc_start: 0.9215 (mmm) cc_final: 0.8565 (mmt) REVERT: F 344 THR cc_start: 0.8510 (m) cc_final: 0.8130 (p) REVERT: G 7 HIS cc_start: 0.9076 (OUTLIER) cc_final: 0.8721 (m-70) REVERT: G 43 TRP cc_start: 0.9424 (OUTLIER) cc_final: 0.9075 (t-100) REVERT: G 154 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7484 (t0) REVERT: G 341 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: H 7 HIS cc_start: 0.9356 (OUTLIER) cc_final: 0.8695 (m-70) REVERT: H 119 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9158 (pp) REVERT: H 174 LEU cc_start: 0.8439 (tp) cc_final: 0.8169 (tp) REVERT: H 208 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: H 221 MET cc_start: 0.8791 (ptm) cc_final: 0.8533 (ptp) REVERT: H 253 ARG cc_start: 0.8704 (ttt-90) cc_final: 0.6482 (mmt-90) REVERT: H 363 MET cc_start: 0.9266 (mmt) cc_final: 0.8903 (mmt) REVERT: I 119 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7985 (pp) REVERT: I 188 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7738 (t80) REVERT: I 193 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8827 (p) REVERT: I 289 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8143 (ptm160) REVERT: I 319 ASN cc_start: 0.8850 (t0) cc_final: 0.8493 (t0) REVERT: J 172 VAL cc_start: 0.8994 (t) cc_final: 0.8792 (p) REVERT: L 8 GLN cc_start: 0.7791 (mt0) cc_final: 0.7507 (mt0) REVERT: L 170 ASP cc_start: 0.8641 (m-30) cc_final: 0.8267 (m-30) REVERT: L 227 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: N 97 LYS cc_start: 0.7846 (tmtt) cc_final: 0.7537 (tptm) REVERT: N 110 ASP cc_start: 0.7810 (t70) cc_final: 0.7420 (t0) REVERT: N 127 ASP cc_start: 0.8593 (t0) cc_final: 0.8211 (m-30) REVERT: N 164 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7486 (pt0) REVERT: N 174 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7424 (mm-30) outliers start: 115 outliers final: 77 residues processed: 403 average time/residue: 0.2101 time to fit residues: 130.7758 Evaluate side-chains 402 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 304 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 524 ARG Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain L residue 227 GLN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 29 optimal weight: 4.9990 chunk 301 optimal weight: 5.9990 chunk 240 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 334 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN J 227 GLN L 98 GLN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.154880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115147 restraints weight = 39630.887| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.78 r_work: 0.3107 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 29812 Z= 0.194 Angle : 0.623 13.646 41120 Z= 0.325 Chirality : 0.042 0.202 4655 Planarity : 0.005 0.063 4869 Dihedral : 18.105 161.009 5543 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 4.17 % Allowed : 18.57 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 0.07 (0.14), residues: 3269 helix: 1.30 (0.14), residues: 1369 sheet: -0.98 (0.22), residues: 450 loop : -0.79 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 45 TYR 0.022 0.002 TYR N 137 PHE 0.014 0.002 PHE C 20 TRP 0.015 0.001 TRP C 132 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00452 (29812) covalent geometry : angle 0.62329 (41120) hydrogen bonds : bond 0.04225 ( 1357) hydrogen bonds : angle 4.66672 ( 3858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 305 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: C 21 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7795 (t0) REVERT: C 24 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7718 (pt) REVERT: C 42 LEU cc_start: 0.8352 (pp) cc_final: 0.8094 (pp) REVERT: C 76 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7796 (t) REVERT: C 98 ARG cc_start: 0.8232 (ptt180) cc_final: 0.7965 (ptt180) REVERT: C 200 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.4629 (pmt-80) REVERT: C 357 ASN cc_start: 0.7970 (m-40) cc_final: 0.7627 (m-40) REVERT: C 421 LEU cc_start: 0.8564 (mt) cc_final: 0.8329 (mt) REVERT: C 434 GLU cc_start: 0.6908 (pp20) cc_final: 0.6631 (pp20) REVERT: C 438 LYS cc_start: 0.9014 (tttp) cc_final: 0.8658 (ttmt) REVERT: C 445 ASN cc_start: 0.7345 (m110) cc_final: 0.6565 (t0) REVERT: C 478 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7147 (tp30) REVERT: C 497 MET cc_start: 0.7250 (mtp) cc_final: 0.6979 (mtp) REVERT: C 524 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7425 (ptm-80) REVERT: D 7 HIS cc_start: 0.9167 (OUTLIER) cc_final: 0.8915 (m-70) REVERT: D 50 GLU cc_start: 0.8579 (tp30) cc_final: 0.8202 (tp30) REVERT: D 54 ARG cc_start: 0.7745 (mtp-110) cc_final: 0.7313 (mtp-110) REVERT: D 233 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8761 (mtp85) REVERT: D 278 MET cc_start: 0.8973 (mmm) cc_final: 0.8551 (mmm) REVERT: E 148 LYS cc_start: 0.8481 (mttp) cc_final: 0.8151 (mmmm) REVERT: F 101 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7352 (mtpt) REVERT: F 119 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8508 (mt) REVERT: F 208 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: F 278 MET cc_start: 0.9242 (mmm) cc_final: 0.8592 (mmt) REVERT: F 344 THR cc_start: 0.8543 (m) cc_final: 0.8151 (p) REVERT: G 7 HIS cc_start: 0.9046 (OUTLIER) cc_final: 0.8677 (m-70) REVERT: G 43 TRP cc_start: 0.9427 (OUTLIER) cc_final: 0.9139 (t-100) REVERT: G 154 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7495 (t0) REVERT: H 7 HIS cc_start: 0.9398 (OUTLIER) cc_final: 0.8663 (m-70) REVERT: H 119 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9196 (pp) REVERT: H 174 LEU cc_start: 0.8455 (tp) cc_final: 0.8207 (tp) REVERT: H 208 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: H 253 ARG cc_start: 0.8774 (ttt-90) cc_final: 0.6570 (mmt-90) REVERT: H 363 MET cc_start: 0.9293 (mmt) cc_final: 0.8961 (mmt) REVERT: I 119 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7995 (pp) REVERT: I 188 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7718 (t80) REVERT: I 193 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8785 (p) REVERT: I 289 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8774 (ptm160) REVERT: I 319 ASN cc_start: 0.8880 (t0) cc_final: 0.8527 (t0) REVERT: J 172 VAL cc_start: 0.9025 (t) cc_final: 0.8793 (p) REVERT: L 8 GLN cc_start: 0.7870 (mt0) cc_final: 0.7594 (mt0) REVERT: L 170 ASP cc_start: 0.8631 (m-30) cc_final: 0.8253 (m-30) REVERT: L 227 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7227 (mp10) REVERT: N 110 ASP cc_start: 0.7853 (t70) cc_final: 0.7457 (t0) REVERT: N 127 ASP cc_start: 0.8634 (t0) cc_final: 0.8245 (m-30) REVERT: N 164 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7522 (pt0) REVERT: N 174 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7446 (mm-30) REVERT: N 225 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7869 (tm-30) outliers start: 111 outliers final: 79 residues processed: 392 average time/residue: 0.2164 time to fit residues: 130.9563 Evaluate side-chains 389 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 288 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 524 ARG Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain E residue 7 HIS Chi-restraints excluded: chain E residue 20 ASP Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 7 HIS Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 225 GLN Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain L residue 227 GLN Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 203 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 149 optimal weight: 6.9990 chunk 119 optimal weight: 0.0970 chunk 8 optimal weight: 20.0000 chunk 336 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN J 23 ASN J 187 GLN J 227 GLN L 98 GLN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117304 restraints weight = 40063.678| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.97 r_work: 0.3099 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29812 Z= 0.158 Angle : 0.602 14.000 41120 Z= 0.313 Chirality : 0.041 0.194 4655 Planarity : 0.005 0.062 4869 Dihedral : 18.075 161.091 5543 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.54 % Rotamer: Outliers : 3.86 % Allowed : 19.06 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: 0.12 (0.14), residues: 3269 helix: 1.36 (0.14), residues: 1369 sheet: -0.95 (0.22), residues: 455 loop : -0.77 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 45 TYR 0.020 0.002 TYR N 137 PHE 0.014 0.002 PHE C 20 TRP 0.017 0.001 TRP D 329 HIS 0.008 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00364 (29812) covalent geometry : angle 0.60207 (41120) hydrogen bonds : bond 0.04062 ( 1357) hydrogen bonds : angle 4.61365 ( 3858) =============================================================================== Job complete usr+sys time: 8520.88 seconds wall clock time: 146 minutes 3.17 seconds (8763.17 seconds total)