Starting phenix.real_space_refine on Thu Mar 5 18:06:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yhs_33837/03_2026/7yhs_33837.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yhs_33837/03_2026/7yhs_33837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yhs_33837/03_2026/7yhs_33837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yhs_33837/03_2026/7yhs_33837.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yhs_33837/03_2026/7yhs_33837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yhs_33837/03_2026/7yhs_33837.map" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.042 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 108 5.49 5 S 25 5.16 5 C 15076 2.51 5 N 4520 2.21 5 O 4867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24596 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3039 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 24, 'TRANS': 398} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 377 Unresolved non-hydrogen angles: 480 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 12, 'GLU:plan': 11, 'ARG:plan': 11, 'GLN:plan1': 11, 'HIS:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 256 Chain: "C" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2240 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 12, 'TRANS': 311} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "E" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2548 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2529 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "H" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2490 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "I" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2514 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain breaks: 1 Chain: "L" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1428 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "M" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1226 Classifications: {'RNA': 58} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 18, 'rna3p_pur': 14, 'rna3p_pyr': 13} Link IDs: {'rna2p': 29, 'rna3p': 28} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 803 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "O" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 244 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 6.08, per 1000 atoms: 0.25 Number of scatterers: 24596 At special positions: 0 Unit cell: (148.41, 138.71, 181.39, 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 25 16.00 P 108 15.00 O 4867 8.00 N 4520 7.00 C 15076 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: 2.39 Conformation dependent library (CDL) restraints added in 980.4 milliseconds 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5482 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 40 sheets defined 30.7% alpha, 17.8% beta 31 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 removed outlier: 4.159A pdb=" N PHE A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 removed outlier: 4.325A pdb=" N LEU A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.083A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.752A pdb=" N GLN A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 162 removed outlier: 3.625A pdb=" N ARG A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.554A pdb=" N ALA A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.896A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.668A pdb=" N LEU A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 removed outlier: 3.731A pdb=" N ILE A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 356 through 364 removed outlier: 4.842A pdb=" N TRP A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 374 through 382 removed outlier: 4.174A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.753A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.912A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 148 removed outlier: 3.596A pdb=" N ARG C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.727A pdb=" N ARG C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.571A pdb=" N ALA C 174 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 223 Processing helix chain 'C' and resid 275 through 283 removed outlier: 3.658A pdb=" N ILE C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 339 through 352 Processing helix chain 'D' and resid 130 through 148 removed outlier: 3.849A pdb=" N ARG D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 208 through 223 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.734A pdb=" N ILE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 33 through 48 removed outlier: 3.902A pdb=" N PHE E 37 " --> pdb=" O SER E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 135 removed outlier: 3.508A pdb=" N GLY E 135 " --> pdb=" O GLN E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 178 Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.954A pdb=" N LEU E 193 " --> pdb=" O ARG E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 removed outlier: 3.617A pdb=" N ALA E 212 " --> pdb=" O THR E 208 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 removed outlier: 3.734A pdb=" N ARG F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.646A pdb=" N ARG F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 224 Processing helix chain 'F' and resid 275 through 284 removed outlier: 3.603A pdb=" N ILE F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 331 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.536A pdb=" N SER G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 293 through 297 removed outlier: 3.786A pdb=" N LEU G 296 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY G 297 " --> pdb=" O ASP G 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 293 through 297' Processing helix chain 'G' and resid 322 through 331 removed outlier: 3.631A pdb=" N LEU G 326 " --> pdb=" O ASP G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 86 through 91 removed outlier: 3.911A pdb=" N ILE H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 224 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 82 through 92 removed outlier: 3.675A pdb=" N LEU I 86 " --> pdb=" O ASP I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 148 removed outlier: 3.772A pdb=" N ARG I 134 " --> pdb=" O ASP I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 163 Processing helix chain 'I' and resid 208 through 222 Processing helix chain 'I' and resid 275 through 283 removed outlier: 3.658A pdb=" N ILE I 279 " --> pdb=" O HIS I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 297 removed outlier: 3.535A pdb=" N LEU I 296 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY I 297 " --> pdb=" O ASP I 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 293 through 297' Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 removed outlier: 3.577A pdb=" N GLN I 342 " --> pdb=" O ALA I 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 14 removed outlier: 4.116A pdb=" N TYR J 12 " --> pdb=" O ASP J 8 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN J 14 " --> pdb=" O ASP J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 78 Processing helix chain 'J' and resid 79 through 100 removed outlier: 3.659A pdb=" N VAL J 83 " --> pdb=" O ARG J 79 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU J 94 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG J 97 " --> pdb=" O ALA J 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 27 Processing helix chain 'L' and resid 108 through 118 removed outlier: 4.474A pdb=" N LEU L 112 " --> pdb=" O ASN L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.432A pdb=" N ALA A 191 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ASN E 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.432A pdb=" N ALA A 191 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ASN E 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE E 279 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALA E 257 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU E 281 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR E 255 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU E 283 " --> pdb=" O ALA E 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA5, first strand: chain 'C' and resid 31 through 33 Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 45 removed outlier: 4.285A pdb=" N VAL C 228 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU C 229 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 176 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG C 191 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 43 through 45 removed outlier: 4.285A pdb=" N VAL C 228 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU C 229 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 176 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA9, first strand: chain 'D' and resid 127 through 128 removed outlier: 4.044A pdb=" N ALA D 127 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AB2, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.878A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 184 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA D 176 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG D 191 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 63 through 70 Processing sheet with id=AB4, first strand: chain 'D' and resid 248 through 249 removed outlier: 4.737A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 56 through 61 removed outlier: 5.411A pdb=" N GLY E 58 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 110 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 56 through 61 removed outlier: 5.411A pdb=" N GLY E 58 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 110 " --> pdb=" O GLY E 60 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA E 103 " --> pdb=" O GLN E 18 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLN E 18 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 105 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER E 16 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL E 107 " --> pdb=" O ARG E 14 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG E 14 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AB8, first strand: chain 'E' and resid 304 through 306 Processing sheet with id=AB9, first strand: chain 'F' and resid 127 through 128 removed outlier: 3.709A pdb=" N ALA F 127 " --> pdb=" O ALA F 32 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.890A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG F 191 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 38 through 39 removed outlier: 5.033A pdb=" N ALA F 272 " --> pdb=" O MET F 44 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 64 through 70 Processing sheet with id=AC4, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AC5, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AC6, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.542A pdb=" N ARG G 117 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG G 191 " --> pdb=" O HIS G 183 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.542A pdb=" N ARG G 117 " --> pdb=" O ASP G 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 64 through 70 Processing sheet with id=AC9, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AD1, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.868A pdb=" N ALA H 127 " --> pdb=" O ALA H 32 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.987A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG H 191 " --> pdb=" O HIS H 183 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AD4, first strand: chain 'H' and resid 63 through 68 Processing sheet with id=AD5, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AD6, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.630A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.897A pdb=" N ALA I 127 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA I 32 " --> pdb=" O ALA I 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 189 through 196 removed outlier: 3.912A pdb=" N ARG I 191 " --> pdb=" O HIS I 183 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA I 42 " --> pdb=" O ILE I 274 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE I 274 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA I 272 " --> pdb=" O MET I 44 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 64 through 70 Processing sheet with id=AE1, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AE2, first strand: chain 'J' and resid 17 through 21 Processing sheet with id=AE3, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.541A pdb=" N LEU L 58 " --> pdb=" O ILE L 7 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 100 through 103 removed outlier: 3.803A pdb=" N PHE L 158 " --> pdb=" O VAL L 103 " (cutoff:3.500A) 887 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3968 1.31 - 1.44: 7269 1.44 - 1.56: 13804 1.56 - 1.69: 216 1.69 - 1.81: 39 Bond restraints: 25296 Sorted by residual: bond pdb=" C PRO L 13 " pdb=" O PRO L 13 " ideal model delta sigma weight residual 1.239 1.187 0.052 1.22e-02 6.72e+03 1.82e+01 bond pdb=" N GLN L 35 " pdb=" CA GLN L 35 " ideal model delta sigma weight residual 1.457 1.482 -0.026 6.40e-03 2.44e+04 1.62e+01 bond pdb=" N ILE L 40 " pdb=" CA ILE L 40 " ideal model delta sigma weight residual 1.458 1.501 -0.044 1.14e-02 7.69e+03 1.47e+01 bond pdb=" C PRO A 229 " pdb=" O PRO A 229 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.26e-02 6.30e+03 1.46e+01 bond pdb=" N GLY L 36 " pdb=" CA GLY L 36 " ideal model delta sigma weight residual 1.445 1.476 -0.032 9.90e-03 1.02e+04 1.03e+01 ... (remaining 25291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 34466 3.38 - 6.75: 354 6.75 - 10.13: 38 10.13 - 13.50: 6 13.50 - 16.88: 2 Bond angle restraints: 34866 Sorted by residual: angle pdb=" N ARG L 39 " pdb=" CA ARG L 39 " pdb=" C ARG L 39 " ideal model delta sigma weight residual 111.14 123.18 -12.04 1.08e+00 8.57e-01 1.24e+02 angle pdb=" N PRO L 17 " pdb=" CA PRO L 17 " pdb=" C PRO L 17 " ideal model delta sigma weight residual 112.47 129.35 -16.88 2.06e+00 2.36e-01 6.71e+01 angle pdb=" N TRP C 168 " pdb=" CA TRP C 168 " pdb=" C TRP C 168 " ideal model delta sigma weight residual 111.14 118.89 -7.75 1.08e+00 8.57e-01 5.15e+01 angle pdb=" C PRO L 13 " pdb=" N GLU L 14 " pdb=" CA GLU L 14 " ideal model delta sigma weight residual 120.28 129.18 -8.90 1.34e+00 5.57e-01 4.41e+01 angle pdb=" C GLN L 19 " pdb=" N LEU L 20 " pdb=" CA LEU L 20 " ideal model delta sigma weight residual 120.38 128.89 -8.51 1.37e+00 5.33e-01 3.86e+01 ... (remaining 34861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 14207 35.45 - 70.89: 803 70.89 - 106.34: 64 106.34 - 141.78: 3 141.78 - 177.23: 7 Dihedral angle restraints: 15084 sinusoidal: 6599 harmonic: 8485 Sorted by residual: dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual 232.00 54.77 177.23 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 39 " pdb=" C1' U M 39 " pdb=" N1 U M 39 " pdb=" C2 U M 39 " ideal model delta sinusoidal sigma weight residual -128.00 48.54 -176.54 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C M 37 " pdb=" C1' C M 37 " pdb=" N1 C M 37 " pdb=" C2 C M 37 " ideal model delta sinusoidal sigma weight residual 232.00 61.19 170.81 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 15081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3482 0.073 - 0.147: 448 0.147 - 0.220: 38 0.220 - 0.293: 5 0.293 - 0.366: 2 Chirality restraints: 3975 Sorted by residual: chirality pdb=" CA PRO L 17 " pdb=" N PRO L 17 " pdb=" C PRO L 17 " pdb=" CB PRO L 17 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB ILE F 72 " pdb=" CA ILE F 72 " pdb=" CG1 ILE F 72 " pdb=" CG2 ILE F 72 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA GLN A 225 " pdb=" N GLN A 225 " pdb=" C GLN A 225 " pdb=" CB GLN A 225 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 3972 not shown) Planarity restraints: 4196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU L 14 " 0.022 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C GLU L 14 " -0.079 2.00e-02 2.50e+03 pdb=" O GLU L 14 " 0.029 2.00e-02 2.50e+03 pdb=" N PHE L 15 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 169 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ARG C 169 " -0.071 2.00e-02 2.50e+03 pdb=" O ARG C 169 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN C 170 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 103 " -0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO F 104 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO F 104 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 104 " -0.044 5.00e-02 4.00e+02 ... (remaining 4193 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 668 2.68 - 3.24: 20904 3.24 - 3.79: 39219 3.79 - 4.35: 50429 4.35 - 4.90: 83111 Nonbonded interactions: 194331 Sorted by model distance: nonbonded pdb=" O PRO L 17 " pdb=" N GLN L 19 " model vdw 2.129 3.120 nonbonded pdb=" O GLN L 19 " pdb=" OG SER L 22 " model vdw 2.219 3.040 nonbonded pdb=" O2' C M 50 " pdb=" OP1 U M 52 " model vdw 2.239 3.040 nonbonded pdb=" N ASP L 38 " pdb=" OD1 ASP L 38 " model vdw 2.261 3.120 nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.279 3.040 ... (remaining 194326 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 'C' and (resid 25 through 51 or (resid 52 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 165 or (resid 166 throu \ gh 171 and (name N or name CA or name C or name O or name CB )) or resid 172 thr \ ough 291 or (resid 292 through 294 and (name N or name CA or name C or name O or \ name CB )) or resid 295 through 319 or (resid 320 through 321 and (name N or na \ me CA or name C or name O or name CB )) or resid 322 through 334 or (resid 335 t \ hrough 336 and (name N or name CA or name C or name O or name CB )) or resid 337 \ through 357)) selection = (chain 'D' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 170 or (resid 171 and (name N or name CA or name C or name O or name CB )) or re \ sid 172 through 250 or resid 263 through 317 or (resid 318 and (name N or name C \ A or name C or name O or name CB )) or resid 319 through 334 or (resid 335 throu \ gh 336 and (name N or name CA or name C or name O or name CB )) or resid 337 thr \ ough 357)) selection = (chain 'F' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 165 or (resid 166 through 171 and (name N or name CA or name C or name O or name \ CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 250 or resid 263 through 291 or (res \ id 292 through 294 and (name N or name CA or name C or name O or name CB )) or r \ esid 295 or (resid 296 and (name N or name CA or name C or name O or name CB )) \ or resid 297 through 317 or (resid 318 and (name N or name CA or name C or name \ O or name CB )) or resid 319 or (resid 320 through 321 and (name N or name CA or \ name C or name O or name CB )) or resid 322 through 334 or (resid 335 through 3 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 337 through \ 357)) selection = (chain 'G' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or re \ sid 204 through 250 or resid 263 through 290 or (resid 291 through 294 and (name \ N or name CA or name C or name O or name CB )) or resid 295 through 317 or (res \ id 318 and (name N or name CA or name C or name O or name CB )) or resid 319 or \ (resid 320 through 321 and (name N or name CA or name C or name O or name CB )) \ or resid 322 through 334 or (resid 335 through 336 and (name N or name CA or nam \ e C or name O or name CB )) or resid 337 through 357)) selection = (chain 'H' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 166 or (resid 167 through 171 and (name N or name CA or name C or name O or name \ CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 250 or resid 263 through 295 or (res \ id 296 and (name N or name CA or name C or name O or name CB )) or resid 297 thr \ ough 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) \ or resid 319 or (resid 320 through 321 and (name N or name CA or name C or name \ O or name CB )) or resid 322 through 334 or (resid 335 through 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 through 357)) selection = (chain 'I' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 165 or (resid 166 through 171 and (name N or name CA or name C or name O or name \ CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 250 or resid 263 through 291 or (res \ id 292 through 294 and (name N or name CA or name C or name O or name CB )) or r \ esid 295 through 317 or (resid 318 and (name N or name CA or name C or name O or \ name CB )) or resid 319 or (resid 320 through 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 357)) } 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: 0.900 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: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.620 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 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 : 0.005 0.057 25296 Z= 0.251 Angle : 0.908 16.880 34866 Z= 0.517 Chirality : 0.050 0.366 3975 Planarity : 0.007 0.081 4196 Dihedral : 20.462 177.230 9602 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.96 % Favored : 91.97 % Rotamer: Outliers : 7.08 % Allowed : 17.46 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.27 (0.12), residues: 2915 helix: -2.92 (0.12), residues: 837 sheet: -0.84 (0.24), residues: 432 loop : -3.51 (0.11), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 69 TYR 0.021 0.002 TYR G 290 PHE 0.019 0.002 PHE C 235 TRP 0.026 0.002 TRP A 228 HIS 0.006 0.001 HIS G 343 Details of bonding type rmsd covalent geometry : bond 0.00493 (25296) covalent geometry : angle 0.90803 (34866) hydrogen bonds : bond 0.13917 ( 940) hydrogen bonds : angle 6.47852 ( 2647) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 322 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7240 (tp) REVERT: A 156 ARG cc_start: 0.6210 (tmt170) cc_final: 0.5110 (tpt170) REVERT: A 193 LEU cc_start: 0.7990 (mt) cc_final: 0.7781 (mt) REVERT: A 226 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: A 390 ARG cc_start: 0.6708 (ttm170) cc_final: 0.6478 (ttm110) REVERT: C 117 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6287 (ptt180) REVERT: C 283 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6311 (mp) REVERT: C 333 ARG cc_start: 0.2880 (OUTLIER) cc_final: 0.2627 (mtm180) REVERT: D 198 LEU cc_start: 0.2158 (OUTLIER) cc_final: 0.1957 (mt) REVERT: E 124 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6624 (pp30) REVERT: E 133 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7362 (tm-30) REVERT: E 138 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7085 (mtt90) REVERT: F 113 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6888 (ttt90) REVERT: G 31 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6614 (tt) REVERT: G 91 GLN cc_start: 0.5825 (OUTLIER) cc_final: 0.5570 (mt0) REVERT: H 117 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7657 (ttm170) REVERT: H 138 LEU cc_start: 0.8000 (mt) cc_final: 0.7774 (mp) REVERT: H 285 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7580 (m) REVERT: L 24 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6495 (tp) REVERT: L 40 ILE cc_start: 0.6289 (OUTLIER) cc_final: 0.5967 (pt) REVERT: L 102 ARG cc_start: 0.5695 (OUTLIER) cc_final: 0.5077 (ppt90) outliers start: 154 outliers final: 93 residues processed: 447 average time/residue: 0.1996 time to fit residues: 133.8273 Evaluate side-chains 409 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 300 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 17 PRO Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 102 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS A 241 GLN A 271 HIS A 283 HIS A 305 GLN C 159 HIS C 183 HIS C 186 GLN C 275 HIS C 277 GLN C 341 GLN C 342 GLN C 348 ASN D 163 ASN D 186 GLN E 82 ASN E 129 GLN E 168 GLN E 194 GLN E 195 GLN F 94 ASN F 102 ASN F 170 ASN F 281 ASN F 316 GLN F 319 GLN G 56 GLN G 94 ASN G 159 HIS H 129 ASN H 329 ASN I 91 GLN I 102 ASN J 27 GLN L 3 HIS L 61 HIS L 104 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.187676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.164583 restraints weight = 36129.082| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.94 r_work: 0.3889 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25296 Z= 0.134 Angle : 0.590 13.209 34866 Z= 0.313 Chirality : 0.040 0.208 3975 Planarity : 0.005 0.058 4196 Dihedral : 19.745 177.242 4892 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.41 % Favored : 92.56 % Rotamer: Outliers : 5.01 % Allowed : 20.45 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.14), residues: 2915 helix: -1.04 (0.16), residues: 839 sheet: -0.44 (0.25), residues: 450 loop : -3.08 (0.12), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 315 TYR 0.018 0.002 TYR C 144 PHE 0.017 0.001 PHE C 323 TRP 0.017 0.001 TRP F 193 HIS 0.011 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00292 (25296) covalent geometry : angle 0.59034 (34866) hydrogen bonds : bond 0.03971 ( 940) hydrogen bonds : angle 4.73278 ( 2647) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 307 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5831 (tt) REVERT: A 63 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7208 (tp) REVERT: A 65 LEU cc_start: 0.6475 (mm) cc_final: 0.6102 (mm) REVERT: A 105 VAL cc_start: 0.6242 (OUTLIER) cc_final: 0.5535 (t) REVERT: A 156 ARG cc_start: 0.6335 (tmt170) cc_final: 0.4775 (tpt170) REVERT: A 193 LEU cc_start: 0.8243 (mt) cc_final: 0.8035 (mt) REVERT: A 235 TYR cc_start: 0.7610 (m-80) cc_final: 0.7155 (m-80) REVERT: A 305 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: A 390 ARG cc_start: 0.7576 (ttm170) cc_final: 0.6998 (mtp-110) REVERT: C 112 VAL cc_start: 0.5323 (OUTLIER) cc_final: 0.5019 (t) REVERT: C 186 GLN cc_start: 0.5766 (OUTLIER) cc_final: 0.5462 (pm20) REVERT: C 330 TRP cc_start: 0.6529 (t-100) cc_final: 0.5950 (t-100) REVERT: E 133 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7621 (tm-30) REVERT: E 138 ARG cc_start: 0.7558 (ptp-170) cc_final: 0.7167 (mtt90) REVERT: F 113 ARG cc_start: 0.7700 (ttt90) cc_final: 0.7325 (ttt90) REVERT: F 289 TRP cc_start: 0.8021 (m-90) cc_final: 0.7717 (m-90) REVERT: H 117 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7740 (ttm170) REVERT: L 24 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6951 (tp) REVERT: L 83 LEU cc_start: 0.6162 (mt) cc_final: 0.5925 (mt) REVERT: L 114 ARG cc_start: 0.6210 (ptm160) cc_final: 0.5086 (ttp-110) REVERT: L 117 MET cc_start: 0.6647 (mmm) cc_final: 0.6164 (mmm) REVERT: L 118 ARG cc_start: 0.7942 (tpm170) cc_final: 0.7081 (tpm170) outliers start: 109 outliers final: 64 residues processed: 396 average time/residue: 0.2033 time to fit residues: 119.3282 Evaluate side-chains 366 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 294 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 51 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 285 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS A 289 HIS A 305 GLN C 170 ASN C 277 GLN E 168 GLN ** E 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS F 91 GLN F 170 ASN G 94 ASN G 129 ASN G 343 HIS I 102 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.181645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.159679 restraints weight = 36061.693| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.59 r_work: 0.3831 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 25296 Z= 0.252 Angle : 0.684 12.643 34866 Z= 0.359 Chirality : 0.044 0.236 3975 Planarity : 0.005 0.065 4196 Dihedral : 19.720 177.083 4778 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.37 % Favored : 90.60 % Rotamer: Outliers : 6.76 % Allowed : 21.09 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.14), residues: 2915 helix: -0.55 (0.17), residues: 839 sheet: -0.37 (0.25), residues: 454 loop : -2.97 (0.13), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 171 TYR 0.025 0.003 TYR D 266 PHE 0.027 0.002 PHE D 245 TRP 0.020 0.002 TRP G 49 HIS 0.009 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00570 (25296) covalent geometry : angle 0.68404 (34866) hydrogen bonds : bond 0.04780 ( 940) hydrogen bonds : angle 4.84224 ( 2647) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 320 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6355 (tt) REVERT: A 105 VAL cc_start: 0.6423 (OUTLIER) cc_final: 0.5749 (t) REVERT: A 156 ARG cc_start: 0.6529 (tmt170) cc_final: 0.4952 (tpt170) REVERT: A 208 GLU cc_start: 0.7326 (tp30) cc_final: 0.7056 (tp30) REVERT: A 235 TYR cc_start: 0.7685 (m-80) cc_final: 0.7329 (m-80) REVERT: C 277 GLN cc_start: 0.6371 (OUTLIER) cc_final: 0.6161 (pm20) REVERT: D 354 VAL cc_start: 0.2256 (OUTLIER) cc_final: 0.2045 (m) REVERT: E 107 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7412 (p) REVERT: E 133 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7670 (tm-30) REVERT: E 138 ARG cc_start: 0.7678 (ptp-170) cc_final: 0.7261 (mtt90) REVERT: E 242 ARG cc_start: 0.6889 (mmm160) cc_final: 0.6593 (mmm160) REVERT: E 304 TYR cc_start: 0.8904 (m-80) cc_final: 0.8650 (m-80) REVERT: F 113 ARG cc_start: 0.7752 (ttt90) cc_final: 0.7425 (ttt90) REVERT: G 31 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6812 (tt) REVERT: G 229 LEU cc_start: 0.7572 (tp) cc_final: 0.7298 (tp) REVERT: H 110 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7855 (tp) REVERT: H 117 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7689 (ttm170) REVERT: I 144 TYR cc_start: 0.8194 (t80) cc_final: 0.7945 (t80) REVERT: I 211 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6664 (mm) REVERT: L 24 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6892 (tp) REVERT: L 83 LEU cc_start: 0.6518 (mt) cc_final: 0.6285 (mt) REVERT: L 114 ARG cc_start: 0.5932 (ptm160) cc_final: 0.4990 (ttp-110) REVERT: L 117 MET cc_start: 0.6432 (mmm) cc_final: 0.6002 (mmm) REVERT: L 118 ARG cc_start: 0.7826 (tpm170) cc_final: 0.7188 (tpm170) outliers start: 147 outliers final: 96 residues processed: 432 average time/residue: 0.1965 time to fit residues: 126.6959 Evaluate side-chains 416 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 310 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 71 optimal weight: 8.9990 chunk 218 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 161 optimal weight: 0.1980 chunk 297 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 193 optimal weight: 0.5980 chunk 270 optimal weight: 7.9990 chunk 274 optimal weight: 0.5980 chunk 280 optimal weight: 0.0980 chunk 237 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN C 275 HIS C 277 GLN C 348 ASN D 342 GLN E 282 ASN F 91 GLN F 163 ASN G 94 ASN H 310 GLN I 102 ASN I 129 ASN I 227 HIS L 19 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.188501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.166099 restraints weight = 35999.466| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.72 r_work: 0.3900 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 25296 Z= 0.108 Angle : 0.553 12.259 34866 Z= 0.291 Chirality : 0.039 0.205 3975 Planarity : 0.004 0.056 4196 Dihedral : 19.333 177.390 4774 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.28 % Favored : 93.69 % Rotamer: Outliers : 5.28 % Allowed : 22.89 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.15), residues: 2915 helix: 0.24 (0.17), residues: 856 sheet: 0.04 (0.25), residues: 450 loop : -2.76 (0.13), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 103 TYR 0.019 0.001 TYR D 266 PHE 0.011 0.001 PHE C 323 TRP 0.018 0.001 TRP C 330 HIS 0.009 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00230 (25296) covalent geometry : angle 0.55281 (34866) hydrogen bonds : bond 0.03307 ( 940) hydrogen bonds : angle 4.24998 ( 2647) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 307 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5733 (mp) REVERT: A 63 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7092 (tp) REVERT: A 65 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6176 (mm) REVERT: A 105 VAL cc_start: 0.6225 (OUTLIER) cc_final: 0.5627 (t) REVERT: A 156 ARG cc_start: 0.6316 (tmt170) cc_final: 0.4826 (tpt170) REVERT: A 235 TYR cc_start: 0.7345 (m-80) cc_final: 0.6824 (m-80) REVERT: A 305 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: A 339 ARG cc_start: 0.6432 (ttm110) cc_final: 0.6166 (ttm110) REVERT: A 361 LEU cc_start: 0.5292 (OUTLIER) cc_final: 0.5086 (tt) REVERT: C 112 VAL cc_start: 0.4972 (OUTLIER) cc_final: 0.4689 (t) REVERT: C 277 GLN cc_start: 0.5966 (OUTLIER) cc_final: 0.5358 (pt0) REVERT: E 133 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7559 (tm-30) REVERT: E 138 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6974 (mtt90) REVERT: F 113 ARG cc_start: 0.7516 (ttt90) cc_final: 0.7156 (ttt90) REVERT: G 31 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6652 (tt) REVERT: I 144 TYR cc_start: 0.8077 (t80) cc_final: 0.7740 (t80) REVERT: I 249 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: L 83 LEU cc_start: 0.6268 (mt) cc_final: 0.6031 (mt) REVERT: L 114 ARG cc_start: 0.5713 (OUTLIER) cc_final: 0.4724 (ttp80) REVERT: L 117 MET cc_start: 0.6168 (mmm) cc_final: 0.5647 (mmm) REVERT: L 118 ARG cc_start: 0.7715 (tpm170) cc_final: 0.7132 (tpm170) outliers start: 115 outliers final: 80 residues processed: 399 average time/residue: 0.1926 time to fit residues: 115.1836 Evaluate side-chains 386 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 294 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 289 TRP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 114 ARG Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 47 optimal weight: 0.0370 chunk 125 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 103 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 291 optimal weight: 4.9990 chunk 35 optimal weight: 0.0670 chunk 279 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN C 186 GLN C 277 GLN E 282 ASN F 91 GLN G 94 ASN G 342 GLN I 102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.186599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.164376 restraints weight = 35942.635| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 1.64 r_work: 0.3904 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25296 Z= 0.116 Angle : 0.553 11.662 34866 Z= 0.290 Chirality : 0.039 0.236 3975 Planarity : 0.004 0.044 4196 Dihedral : 19.237 177.063 4768 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.24 % Favored : 92.73 % Rotamer: Outliers : 5.19 % Allowed : 23.62 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.15), residues: 2915 helix: 0.54 (0.18), residues: 857 sheet: 0.16 (0.25), residues: 461 loop : -2.66 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 194 TYR 0.016 0.001 TYR D 266 PHE 0.011 0.001 PHE F 166 TRP 0.015 0.001 TRP C 330 HIS 0.010 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00255 (25296) covalent geometry : angle 0.55347 (34866) hydrogen bonds : bond 0.03359 ( 940) hydrogen bonds : angle 4.14613 ( 2647) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 286 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5819 (mp) REVERT: A 63 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7249 (tp) REVERT: A 65 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6382 (mm) REVERT: A 108 VAL cc_start: 0.6140 (OUTLIER) cc_final: 0.5899 (t) REVERT: A 156 ARG cc_start: 0.6451 (tmt170) cc_final: 0.4897 (tpt170) REVERT: A 208 GLU cc_start: 0.7180 (tp30) cc_final: 0.6953 (tp30) REVERT: A 235 TYR cc_start: 0.7590 (m-80) cc_final: 0.7121 (m-80) REVERT: A 305 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.7059 (mp10) REVERT: A 339 ARG cc_start: 0.6821 (ttm110) cc_final: 0.6543 (ttm110) REVERT: A 361 LEU cc_start: 0.5511 (OUTLIER) cc_final: 0.5294 (tt) REVERT: A 386 GLU cc_start: 0.6456 (pp20) cc_final: 0.6236 (pp20) REVERT: C 112 VAL cc_start: 0.5209 (OUTLIER) cc_final: 0.4931 (t) REVERT: E 133 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7708 (tm-30) REVERT: E 138 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7094 (mtt90) REVERT: F 35 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.6121 (ptp90) REVERT: F 113 ARG cc_start: 0.7731 (ttt90) cc_final: 0.7408 (ttt90) REVERT: G 31 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6742 (tt) REVERT: H 130 ASP cc_start: 0.6387 (t70) cc_final: 0.6121 (t70) REVERT: I 249 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: L 1 MET cc_start: 0.3300 (OUTLIER) cc_final: 0.2739 (mmm) REVERT: L 83 LEU cc_start: 0.6542 (mt) cc_final: 0.6223 (mt) REVERT: L 117 MET cc_start: 0.6287 (mmm) cc_final: 0.5888 (mmm) outliers start: 113 outliers final: 89 residues processed: 380 average time/residue: 0.1866 time to fit residues: 106.6585 Evaluate side-chains 383 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 282 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 0.0020 chunk 84 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 186 optimal weight: 3.9990 chunk 285 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN C 277 GLN G 94 ASN I 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.187090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.164888 restraints weight = 36018.971| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.64 r_work: 0.3916 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25296 Z= 0.111 Angle : 0.543 11.145 34866 Z= 0.285 Chirality : 0.039 0.231 3975 Planarity : 0.004 0.047 4196 Dihedral : 19.142 177.083 4760 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.86 % Favored : 93.10 % Rotamer: Outliers : 5.24 % Allowed : 23.67 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.15), residues: 2915 helix: 0.80 (0.18), residues: 853 sheet: 0.31 (0.25), residues: 458 loop : -2.56 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 194 TYR 0.017 0.001 TYR C 290 PHE 0.010 0.001 PHE G 114 TRP 0.014 0.001 TRP C 330 HIS 0.010 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00241 (25296) covalent geometry : angle 0.54303 (34866) hydrogen bonds : bond 0.03224 ( 940) hydrogen bonds : angle 4.05682 ( 2647) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 279 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5799 (mp) REVERT: A 63 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7226 (tp) REVERT: A 65 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6382 (mm) REVERT: A 156 ARG cc_start: 0.6441 (tmt170) cc_final: 0.4903 (tpt170) REVERT: A 208 GLU cc_start: 0.7157 (tp30) cc_final: 0.6936 (tp30) REVERT: A 235 TYR cc_start: 0.7571 (m-80) cc_final: 0.7064 (m-80) REVERT: A 285 SER cc_start: 0.6229 (t) cc_final: 0.5885 (p) REVERT: A 305 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7103 (mp10) REVERT: A 339 ARG cc_start: 0.6807 (ttm110) cc_final: 0.6526 (ttm110) REVERT: A 361 LEU cc_start: 0.5494 (OUTLIER) cc_final: 0.5287 (tt) REVERT: C 112 VAL cc_start: 0.5166 (OUTLIER) cc_final: 0.4888 (t) REVERT: C 333 ARG cc_start: 0.3341 (OUTLIER) cc_final: 0.2987 (mtm180) REVERT: E 133 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7121 (tm-30) REVERT: E 138 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7027 (mtt90) REVERT: E 158 GLU cc_start: 0.5402 (OUTLIER) cc_final: 0.4923 (tp30) REVERT: F 35 ARG cc_start: 0.6603 (OUTLIER) cc_final: 0.6117 (ptp90) REVERT: F 113 ARG cc_start: 0.7680 (ttt90) cc_final: 0.7367 (ttt90) REVERT: G 31 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6728 (tt) REVERT: H 130 ASP cc_start: 0.6426 (t70) cc_final: 0.6101 (t0) REVERT: I 144 TYR cc_start: 0.8144 (t80) cc_final: 0.7892 (t80) REVERT: I 249 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6509 (mp0) REVERT: L 1 MET cc_start: 0.3045 (mmm) cc_final: 0.2569 (mmm) REVERT: L 83 LEU cc_start: 0.6384 (mt) cc_final: 0.6159 (mt) REVERT: L 117 MET cc_start: 0.6175 (mmm) cc_final: 0.5796 (mmm) outliers start: 114 outliers final: 85 residues processed: 373 average time/residue: 0.1983 time to fit residues: 110.1043 Evaluate side-chains 372 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 275 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 289 TRP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 198 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 120 optimal weight: 0.0040 chunk 193 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 132 optimal weight: 0.3980 chunk 238 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 167 optimal weight: 0.4980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN C 170 ASN C 186 GLN C 227 HIS F 129 ASN I 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.187068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.164714 restraints weight = 36075.720| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 1.68 r_work: 0.3915 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25296 Z= 0.114 Angle : 0.545 10.093 34866 Z= 0.285 Chirality : 0.039 0.240 3975 Planarity : 0.004 0.050 4196 Dihedral : 19.062 177.068 4751 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.14 % Favored : 92.83 % Rotamer: Outliers : 5.33 % Allowed : 23.90 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.15), residues: 2915 helix: 0.91 (0.18), residues: 853 sheet: 0.36 (0.25), residues: 459 loop : -2.51 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 194 TYR 0.018 0.001 TYR D 266 PHE 0.011 0.001 PHE E 321 TRP 0.015 0.001 TRP C 330 HIS 0.011 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00249 (25296) covalent geometry : angle 0.54514 (34866) hydrogen bonds : bond 0.03208 ( 940) hydrogen bonds : angle 4.02876 ( 2647) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 277 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5792 (mp) REVERT: A 63 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7230 (tp) REVERT: A 65 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6382 (mm) REVERT: A 156 ARG cc_start: 0.6449 (tmt170) cc_final: 0.4871 (tpt170) REVERT: A 208 GLU cc_start: 0.7184 (tp30) cc_final: 0.6971 (tp30) REVERT: A 235 TYR cc_start: 0.7595 (m-80) cc_final: 0.7069 (m-80) REVERT: A 285 SER cc_start: 0.6192 (t) cc_final: 0.5818 (p) REVERT: A 305 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: A 339 ARG cc_start: 0.6832 (ttm110) cc_final: 0.6548 (ttm110) REVERT: A 361 LEU cc_start: 0.5508 (OUTLIER) cc_final: 0.5302 (tt) REVERT: C 112 VAL cc_start: 0.5131 (OUTLIER) cc_final: 0.4852 (t) REVERT: C 333 ARG cc_start: 0.3366 (OUTLIER) cc_final: 0.3013 (mtm180) REVERT: E 107 VAL cc_start: 0.7307 (p) cc_final: 0.5756 (t) REVERT: E 138 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7012 (mtt90) REVERT: E 158 GLU cc_start: 0.5451 (OUTLIER) cc_final: 0.4942 (tp30) REVERT: F 35 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.6110 (ptp90) REVERT: F 113 ARG cc_start: 0.7644 (ttt90) cc_final: 0.7344 (ttt90) REVERT: G 31 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6723 (tt) REVERT: H 130 ASP cc_start: 0.6594 (t70) cc_final: 0.6334 (t0) REVERT: I 249 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: L 1 MET cc_start: 0.2831 (mmm) cc_final: 0.2479 (mmm) REVERT: L 83 LEU cc_start: 0.6535 (mt) cc_final: 0.6295 (mt) REVERT: L 117 MET cc_start: 0.6196 (mmm) cc_final: 0.5831 (mmm) outliers start: 116 outliers final: 92 residues processed: 375 average time/residue: 0.1924 time to fit residues: 107.9727 Evaluate side-chains 379 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 275 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 129 ASN Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 289 TRP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 154 optimal weight: 2.9990 chunk 279 optimal weight: 0.0970 chunk 144 optimal weight: 3.9990 chunk 2 optimal weight: 0.0170 chunk 100 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN C 227 HIS F 129 ASN G 96 GLN I 102 ASN ** L 154 HIS ** 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 = 0.4299 r_free = 0.4299 target = 0.187152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.164725 restraints weight = 36059.630| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.64 r_work: 0.3918 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25296 Z= 0.117 Angle : 0.549 9.394 34866 Z= 0.286 Chirality : 0.039 0.250 3975 Planarity : 0.004 0.057 4196 Dihedral : 19.027 177.036 4747 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.96 % Favored : 93.00 % Rotamer: Outliers : 5.65 % Allowed : 23.53 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 2915 helix: 0.98 (0.18), residues: 853 sheet: 0.41 (0.25), residues: 459 loop : -2.48 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 194 TYR 0.017 0.001 TYR D 266 PHE 0.012 0.001 PHE E 321 TRP 0.015 0.001 TRP C 330 HIS 0.011 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00257 (25296) covalent geometry : angle 0.54872 (34866) hydrogen bonds : bond 0.03183 ( 940) hydrogen bonds : angle 4.02895 ( 2647) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 278 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5785 (mp) REVERT: A 63 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7216 (tp) REVERT: A 65 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6380 (mm) REVERT: A 156 ARG cc_start: 0.6468 (tmt170) cc_final: 0.4874 (tpt170) REVERT: A 208 GLU cc_start: 0.7184 (tp30) cc_final: 0.6971 (tp30) REVERT: A 235 TYR cc_start: 0.7578 (m-80) cc_final: 0.7108 (m-80) REVERT: A 305 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: A 339 ARG cc_start: 0.6816 (ttm110) cc_final: 0.6538 (ttm110) REVERT: A 361 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.5270 (tt) REVERT: C 112 VAL cc_start: 0.5184 (OUTLIER) cc_final: 0.4892 (t) REVERT: C 227 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6657 (p-80) REVERT: C 333 ARG cc_start: 0.3504 (OUTLIER) cc_final: 0.3178 (mtm180) REVERT: E 107 VAL cc_start: 0.7310 (p) cc_final: 0.5765 (t) REVERT: E 138 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7108 (mtt90) REVERT: E 158 GLU cc_start: 0.5443 (OUTLIER) cc_final: 0.4963 (tp30) REVERT: F 35 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.6096 (ptp90) REVERT: F 113 ARG cc_start: 0.7633 (ttt90) cc_final: 0.7331 (ttt90) REVERT: G 31 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6705 (tt) REVERT: H 130 ASP cc_start: 0.6578 (t70) cc_final: 0.6321 (t0) REVERT: I 144 TYR cc_start: 0.8170 (t80) cc_final: 0.7872 (t80) REVERT: I 249 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: L 1 MET cc_start: 0.2712 (mmm) cc_final: 0.2446 (mmm) REVERT: L 83 LEU cc_start: 0.6529 (mt) cc_final: 0.6296 (mt) REVERT: L 117 MET cc_start: 0.6175 (mmm) cc_final: 0.5825 (mmm) outliers start: 123 outliers final: 100 residues processed: 383 average time/residue: 0.1951 time to fit residues: 111.7039 Evaluate side-chains 387 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 274 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 129 ASN Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 289 TRP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 232 optimal weight: 3.9990 chunk 164 optimal weight: 0.4980 chunk 226 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 245 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 17 optimal weight: 0.0270 chunk 111 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN D 148 GLN E 104 HIS G 94 ASN I 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.186557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.164648 restraints weight = 36045.664| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.62 r_work: 0.3877 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25296 Z= 0.131 Angle : 0.564 9.488 34866 Z= 0.292 Chirality : 0.040 0.258 3975 Planarity : 0.004 0.060 4196 Dihedral : 19.015 176.982 4747 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.38 % Favored : 92.59 % Rotamer: Outliers : 5.42 % Allowed : 23.90 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.15), residues: 2915 helix: 0.93 (0.18), residues: 860 sheet: 0.40 (0.25), residues: 457 loop : -2.47 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 194 TYR 0.018 0.002 TYR D 266 PHE 0.018 0.001 PHE L 44 TRP 0.015 0.001 TRP C 330 HIS 0.011 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00290 (25296) covalent geometry : angle 0.56398 (34866) hydrogen bonds : bond 0.03309 ( 940) hydrogen bonds : angle 4.07660 ( 2647) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 281 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5667 (mp) REVERT: A 63 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7100 (tp) REVERT: A 65 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6290 (mm) REVERT: A 105 VAL cc_start: 0.6126 (OUTLIER) cc_final: 0.5491 (t) REVERT: A 156 ARG cc_start: 0.6410 (tmt170) cc_final: 0.4889 (tpt170) REVERT: A 208 GLU cc_start: 0.7084 (tp30) cc_final: 0.6879 (tp30) REVERT: A 235 TYR cc_start: 0.7380 (m-80) cc_final: 0.6911 (m-80) REVERT: A 305 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6986 (mp10) REVERT: A 339 ARG cc_start: 0.6561 (ttm110) cc_final: 0.6288 (ttm110) REVERT: C 112 VAL cc_start: 0.4941 (OUTLIER) cc_final: 0.4675 (t) REVERT: C 333 ARG cc_start: 0.3465 (OUTLIER) cc_final: 0.3149 (mtm180) REVERT: E 107 VAL cc_start: 0.7267 (p) cc_final: 0.5773 (t) REVERT: E 138 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7065 (mtt90) REVERT: E 158 GLU cc_start: 0.5338 (OUTLIER) cc_final: 0.4846 (tp30) REVERT: F 35 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.6075 (ptp90) REVERT: F 113 ARG cc_start: 0.7521 (ttt90) cc_final: 0.7229 (ttt90) REVERT: F 249 GLU cc_start: 0.7331 (mm-30) cc_final: 0.7119 (mm-30) REVERT: G 31 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6715 (tt) REVERT: G 229 LEU cc_start: 0.7343 (tp) cc_final: 0.7075 (tp) REVERT: H 130 ASP cc_start: 0.6342 (t70) cc_final: 0.6081 (t0) REVERT: I 144 TYR cc_start: 0.8172 (t80) cc_final: 0.7928 (t80) REVERT: I 249 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: I 265 LEU cc_start: 0.8071 (mt) cc_final: 0.7622 (tp) REVERT: L 83 LEU cc_start: 0.6436 (mt) cc_final: 0.6219 (mt) REVERT: L 113 ARG cc_start: 0.6232 (ptp90) cc_final: 0.5925 (ptp90) REVERT: L 117 MET cc_start: 0.5959 (mmm) cc_final: 0.5658 (mmm) REVERT: L 118 ARG cc_start: 0.7066 (mtt180) cc_final: 0.6672 (mtt180) outliers start: 118 outliers final: 101 residues processed: 377 average time/residue: 0.1950 time to fit residues: 109.8648 Evaluate side-chains 393 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 280 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 289 TRP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 107 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 134 optimal weight: 0.1980 chunk 184 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 288 optimal weight: 0.0570 chunk 8 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 114 optimal weight: 0.3980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN I 102 ASN ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.188384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.166247 restraints weight = 36196.541| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.64 r_work: 0.3933 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25296 Z= 0.102 Angle : 0.541 9.840 34866 Z= 0.280 Chirality : 0.039 0.260 3975 Planarity : 0.004 0.063 4196 Dihedral : 18.921 177.314 4747 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.79 % Favored : 93.17 % Rotamer: Outliers : 5.06 % Allowed : 24.13 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.15), residues: 2915 helix: 1.09 (0.18), residues: 866 sheet: 0.50 (0.25), residues: 452 loop : -2.44 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 194 TYR 0.019 0.001 TYR D 266 PHE 0.013 0.001 PHE L 44 TRP 0.019 0.001 TRP C 330 HIS 0.011 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00218 (25296) covalent geometry : angle 0.54127 (34866) hydrogen bonds : bond 0.03008 ( 940) hydrogen bonds : angle 3.94880 ( 2647) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 274 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.5038 (OUTLIER) cc_final: 0.4675 (mp) REVERT: A 25 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5705 (mp) REVERT: A 63 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7219 (tp) REVERT: A 65 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6412 (mm) REVERT: A 105 VAL cc_start: 0.6184 (OUTLIER) cc_final: 0.5494 (t) REVERT: A 156 ARG cc_start: 0.6448 (tmt170) cc_final: 0.4852 (tpt170) REVERT: A 208 GLU cc_start: 0.7181 (tp30) cc_final: 0.6951 (tp30) REVERT: A 235 TYR cc_start: 0.7564 (m-80) cc_final: 0.7090 (m-80) REVERT: A 305 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7160 (mp10) REVERT: A 339 ARG cc_start: 0.6795 (ttm110) cc_final: 0.6513 (ttm110) REVERT: C 112 VAL cc_start: 0.5140 (OUTLIER) cc_final: 0.4859 (t) REVERT: C 333 ARG cc_start: 0.3583 (OUTLIER) cc_final: 0.3304 (mtm180) REVERT: E 107 VAL cc_start: 0.7260 (p) cc_final: 0.5628 (t) REVERT: E 138 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6974 (mtt90) REVERT: E 158 GLU cc_start: 0.5374 (OUTLIER) cc_final: 0.4925 (tp30) REVERT: F 35 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.6218 (ptp90) REVERT: F 113 ARG cc_start: 0.7650 (ttt90) cc_final: 0.7332 (ttt90) REVERT: F 233 VAL cc_start: 0.8054 (t) cc_final: 0.7634 (m) REVERT: G 31 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6772 (tt) REVERT: H 34 GLU cc_start: 0.7079 (tp30) cc_final: 0.6854 (tp30) REVERT: H 130 ASP cc_start: 0.6572 (t70) cc_final: 0.6320 (t0) REVERT: H 155 ARG cc_start: 0.7658 (ttp80) cc_final: 0.7287 (ttp80) REVERT: I 249 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: L 83 LEU cc_start: 0.6506 (mt) cc_final: 0.6254 (mt) REVERT: L 113 ARG cc_start: 0.6403 (ptp90) cc_final: 0.6100 (ptp90) REVERT: L 117 MET cc_start: 0.6189 (mmm) cc_final: 0.5894 (mmm) REVERT: L 118 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6723 (mtt180) outliers start: 110 outliers final: 89 residues processed: 365 average time/residue: 0.1906 time to fit residues: 103.3029 Evaluate side-chains 372 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 270 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 289 TRP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 211 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 297 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN I 102 ASN ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.186221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.164404 restraints weight = 35985.379| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 1.66 r_work: 0.3869 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25296 Z= 0.143 Angle : 0.574 12.117 34866 Z= 0.297 Chirality : 0.040 0.275 3975 Planarity : 0.004 0.061 4196 Dihedral : 18.930 176.773 4747 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.72 % Favored : 92.25 % Rotamer: Outliers : 5.15 % Allowed : 24.03 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 2915 helix: 0.95 (0.18), residues: 871 sheet: 0.44 (0.25), residues: 453 loop : -2.45 (0.14), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 194 TYR 0.017 0.002 TYR D 266 PHE 0.020 0.002 PHE D 245 TRP 0.017 0.001 TRP C 330 HIS 0.011 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00320 (25296) covalent geometry : angle 0.57356 (34866) hydrogen bonds : bond 0.03408 ( 940) hydrogen bonds : angle 4.08351 ( 2647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6262.94 seconds wall clock time: 107 minutes 39.91 seconds (6459.91 seconds total)