Starting phenix.real_space_refine on Sun Aug 24 09:26:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txr_41704/08_2025/8txr_41704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txr_41704/08_2025/8txr_41704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8txr_41704/08_2025/8txr_41704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txr_41704/08_2025/8txr_41704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8txr_41704/08_2025/8txr_41704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txr_41704/08_2025/8txr_41704.map" } resolution = 3.8 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= -0.055 sd= 0.214 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 11828 2.51 5 N 3498 2.21 5 O 3656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19020 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3432 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain breaks: 2 Chain: "C" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3458 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 411} Chain breaks: 2 Chain: "i" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 482 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "c" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 457 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "g" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 457 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "h" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 466 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "a" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 370 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "b" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 495 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "B" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2367 Classifications: {'peptide': 297} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 281} Chain breaks: 1 Chain: "o" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "p" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 473 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "D" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2367 Classifications: {'peptide': 297} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 281} Chain breaks: 1 Chain: "m" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 470 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "n" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 470 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "j" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 465 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "k" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 473 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "l" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 466 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "d" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 473 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "e" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 482 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "f" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 466 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Time building chain proxies: 4.82, per 1000 atoms: 0.25 Number of scatterers: 19020 At special positions: 0 Unit cell: (103, 106, 348, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 3656 8.00 N 3498 7.00 C 11828 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: 1.58 Conformation dependent library (CDL) restraints added in 884.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4540 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 10 sheets defined 66.4% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 12 through 27 removed outlier: 3.648A pdb=" N LEU A 21 " --> pdb=" O GLN A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 4.354A pdb=" N ARG A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 removed outlier: 3.617A pdb=" N GLU A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 150 through 164 removed outlier: 4.014A pdb=" N HIS A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.757A pdb=" N GLN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.786A pdb=" N TRP A 214 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER A 215 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.881A pdb=" N PHE A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 264 removed outlier: 3.705A pdb=" N ALA A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 306 removed outlier: 3.974A pdb=" N GLN A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN A 306 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 350 removed outlier: 3.830A pdb=" N LYS A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 396 Processing helix chain 'C' and resid 12 through 27 Processing helix chain 'C' and resid 63 through 68 Processing helix chain 'C' and resid 110 through 125 removed outlier: 3.514A pdb=" N LYS C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 164 removed outlier: 4.183A pdb=" N HIS C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 196 removed outlier: 4.259A pdb=" N GLY C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C 190 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 217 Processing helix chain 'C' and resid 218 through 228 removed outlier: 4.151A pdb=" N ALA C 222 " --> pdb=" O ASP C 218 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 removed outlier: 3.765A pdb=" N PHE C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.786A pdb=" N ALA C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 305 removed outlier: 3.578A pdb=" N LEU C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 305 " --> pdb=" O HIS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 351 removed outlier: 3.523A pdb=" N GLN C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 322 " --> pdb=" O MET C 318 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 344 " --> pdb=" O GLN C 340 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 395 removed outlier: 3.534A pdb=" N ALA C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 423 Processing helix chain 'i' and resid 10 through 28 removed outlier: 3.603A pdb=" N ALA i 14 " --> pdb=" O SER i 10 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU i 15 " --> pdb=" O PHE i 11 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER i 16 " --> pdb=" O GLU i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 31 through 65 removed outlier: 3.550A pdb=" N GLN i 44 " --> pdb=" O GLU i 40 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE i 62 " --> pdb=" O GLN i 58 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 27 Processing helix chain 'c' and resid 31 through 34 Processing helix chain 'c' and resid 35 through 60 removed outlier: 3.539A pdb=" N GLN c 58 " --> pdb=" O GLN c 54 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 65 Processing helix chain 'g' and resid 10 through 28 Processing helix chain 'g' and resid 31 through 54 removed outlier: 3.738A pdb=" N ASN g 37 " --> pdb=" O GLU g 33 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS g 52 " --> pdb=" O GLN g 48 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU g 53 " --> pdb=" O GLY g 49 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 28 removed outlier: 3.523A pdb=" N GLN h 20 " --> pdb=" O SER h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 31 through 65 removed outlier: 3.548A pdb=" N GLN h 44 " --> pdb=" O GLU h 40 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS h 52 " --> pdb=" O GLN h 48 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU h 53 " --> pdb=" O GLY h 49 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE h 62 " --> pdb=" O GLN h 58 " (cutoff:3.500A) Processing helix chain 'a' and resid 10 through 27 Processing helix chain 'a' and resid 31 through 55 removed outlier: 3.951A pdb=" N LYS a 52 " --> pdb=" O GLN a 48 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 26 Processing helix chain 'b' and resid 31 through 65 removed outlier: 3.636A pdb=" N ARG b 41 " --> pdb=" O ASN b 37 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER b 65 " --> pdb=" O GLN b 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 28 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.623A pdb=" N LYS B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.681A pdb=" N HIS B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.780A pdb=" N GLN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 226 Processing helix chain 'B' and resid 243 through 249 removed outlier: 3.786A pdb=" N PHE B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 264 removed outlier: 3.551A pdb=" N ALA B 260 " --> pdb=" O PRO B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 306 Processing helix chain 'o' and resid 11 through 26 Processing helix chain 'o' and resid 31 through 56 removed outlier: 3.826A pdb=" N ALA o 56 " --> pdb=" O LYS o 52 " (cutoff:3.500A) Processing helix chain 'p' and resid 10 through 27 Processing helix chain 'p' and resid 35 through 65 removed outlier: 3.592A pdb=" N GLU p 40 " --> pdb=" O LEU p 36 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG p 41 " --> pdb=" O ASN p 37 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL p 43 " --> pdb=" O PHE p 39 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU p 63 " --> pdb=" O ARG p 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 28 Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 209 through 217 removed outlier: 3.648A pdb=" N PHE D 216 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 228 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 255 through 264 Processing helix chain 'D' and resid 266 through 306 Processing helix chain 'm' and resid 11 through 28 removed outlier: 3.916A pdb=" N GLY m 28 " --> pdb=" O ARG m 24 " (cutoff:3.500A) Processing helix chain 'm' and resid 31 through 59 Processing helix chain 'n' and resid 11 through 28 removed outlier: 4.077A pdb=" N SER n 16 " --> pdb=" O GLU n 12 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN n 20 " --> pdb=" O SER n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 31 through 64 removed outlier: 3.723A pdb=" N GLN n 54 " --> pdb=" O GLN n 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU n 63 " --> pdb=" O ARG n 59 " (cutoff:3.500A) Processing helix chain 'j' and resid 10 through 27 removed outlier: 3.656A pdb=" N SER j 27 " --> pdb=" O THR j 23 " (cutoff:3.500A) Processing helix chain 'j' and resid 31 through 65 removed outlier: 3.646A pdb=" N ARG j 41 " --> pdb=" O ASN j 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY j 42 " --> pdb=" O GLU j 38 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS j 52 " --> pdb=" O GLN j 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU j 53 " --> pdb=" O GLY j 49 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE j 62 " --> pdb=" O GLN j 58 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 27 Processing helix chain 'k' and resid 31 through 65 removed outlier: 3.869A pdb=" N GLN k 44 " --> pdb=" O GLU k 40 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU k 53 " --> pdb=" O GLY k 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 10 through 28 removed outlier: 3.534A pdb=" N GLN l 20 " --> pdb=" O SER l 16 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY l 28 " --> pdb=" O ARG l 24 " (cutoff:3.500A) Processing helix chain 'l' and resid 31 through 65 removed outlier: 3.981A pdb=" N ASN l 37 " --> pdb=" O GLU l 33 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU l 40 " --> pdb=" O LEU l 36 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG l 41 " --> pdb=" O ASN l 37 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN l 44 " --> pdb=" O GLU l 40 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS l 52 " --> pdb=" O GLN l 48 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU l 53 " --> pdb=" O GLY l 49 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN l 58 " --> pdb=" O GLN l 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 10 through 26 removed outlier: 3.697A pdb=" N GLN d 20 " --> pdb=" O SER d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 65 removed outlier: 3.510A pdb=" N LEU d 36 " --> pdb=" O LEU d 32 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN d 37 " --> pdb=" O GLU d 33 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG d 59 " --> pdb=" O GLN d 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 27 removed outlier: 3.778A pdb=" N SER e 27 " --> pdb=" O THR e 23 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 65 removed outlier: 3.770A pdb=" N ASN e 37 " --> pdb=" O GLU e 33 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU e 40 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG e 41 " --> pdb=" O ASN e 37 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS e 52 " --> pdb=" O GLN e 48 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN e 61 " --> pdb=" O GLU e 57 " (cutoff:3.500A) Processing helix chain 'f' and resid 10 through 27 Processing helix chain 'f' and resid 31 through 65 removed outlier: 3.796A pdb=" N ASN f 37 " --> pdb=" O GLU f 33 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN f 44 " --> pdb=" O GLU f 40 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU f 45 " --> pdb=" O ARG f 41 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN f 48 " --> pdb=" O GLN f 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.840A pdb=" N LEU C 81 " --> pdb=" O MET C 102 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N MET C 102 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG C 83 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N TYR C 95 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG C 59 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR C 48 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE C 39 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 35 " --> pdb=" O LYS C 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 9 through 11 removed outlier: 6.520A pdb=" N TRP A 31 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 81 " --> pdb=" O MET A 102 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET A 102 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG A 83 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N GLN A 57 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N ILE A 97 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG A 59 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL A 99 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA A 61 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N SER A 101 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR A 50 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN A 38 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LYS A 52 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE A 36 " --> pdb=" O LYS A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 removed outlier: 6.549A pdb=" N LEU A 201 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA A 235 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL A 203 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A 204 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 142 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N TYR A 172 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 144 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 411 removed outlier: 4.603A pdb=" N GLU A 441 " --> pdb=" O GLU C 441 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU C 441 " --> pdb=" O GLU A 441 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU C 439 " --> pdb=" O LYS A 443 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE A 445 " --> pdb=" O TRP C 437 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N TRP C 437 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 408 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 408 through 411 removed outlier: 3.523A pdb=" N TRP A 437 " --> pdb=" O GLN C 446 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 439 " --> pdb=" O ASN C 444 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN C 444 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 169 through 173 removed outlier: 6.290A pdb=" N LEU C 201 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 251 " --> pdb=" O VAL C 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 11 removed outlier: 6.635A pdb=" N LEU D 81 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET D 102 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG D 83 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N GLN D 57 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N ILE D 97 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG D 59 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL D 99 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA D 61 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N SER D 101 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 56 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR D 48 " --> pdb=" O PHE D 39 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE D 39 " --> pdb=" O TYR D 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 11 removed outlier: 9.258A pdb=" N PHE D 10 " --> pdb=" O GLN B 29 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP B 31 " --> pdb=" O PHE D 10 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 101 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN B 85 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL B 99 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 87 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE B 97 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR B 89 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR B 95 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 9.527A pdb=" N GLN B 57 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N ILE B 97 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG B 59 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL B 99 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA B 61 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER B 101 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 50 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASN B 38 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS B 52 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE B 36 " --> pdb=" O LYS B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 251 through 252 removed outlier: 3.623A pdb=" N LEU B 251 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 201 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ALA B 235 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL B 203 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY B 143 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLY B 204 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE B 145 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 142 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N TYR B 172 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 144 " --> pdb=" O TYR B 172 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN o 61 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 173 removed outlier: 6.396A pdb=" N LEU D 201 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 251 " --> pdb=" O VAL D 232 " (cutoff:3.500A) 1306 hydrogen bonds defined for protein. 3831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6752 1.34 - 1.46: 2617 1.46 - 1.57: 9833 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 19266 Sorted by residual: bond pdb=" N SER n 10 " pdb=" CA SER n 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N ALA h 9 " pdb=" CA ALA h 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N SER o 10 " pdb=" CA SER o 10 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N SER m 10 " pdb=" CA SER m 10 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N ALA b 7 " pdb=" CA ALA b 7 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 19261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 24564 0.88 - 1.75: 1205 1.75 - 2.63: 132 2.63 - 3.50: 63 3.50 - 4.38: 33 Bond angle restraints: 25997 Sorted by residual: angle pdb=" CA TRP B 47 " pdb=" CB TRP B 47 " pdb=" CG TRP B 47 " ideal model delta sigma weight residual 113.60 117.86 -4.26 1.90e+00 2.77e-01 5.02e+00 angle pdb=" N ASP B 53 " pdb=" CA ASP B 53 " pdb=" C ASP B 53 " ideal model delta sigma weight residual 110.80 106.99 3.81 2.13e+00 2.20e-01 3.20e+00 angle pdb=" N SER C 397 " pdb=" CA SER C 397 " pdb=" C SER C 397 " ideal model delta sigma weight residual 109.81 113.56 -3.75 2.21e+00 2.05e-01 2.88e+00 angle pdb=" N THR A 55 " pdb=" CA THR A 55 " pdb=" C THR A 55 " ideal model delta sigma weight residual 110.80 114.25 -3.45 2.13e+00 2.20e-01 2.62e+00 angle pdb=" C THR B 227 " pdb=" CA THR B 227 " pdb=" CB THR B 227 " ideal model delta sigma weight residual 111.06 108.24 2.82 1.83e+00 2.99e-01 2.38e+00 ... (remaining 25992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 11269 17.59 - 35.18: 560 35.18 - 52.77: 121 52.77 - 70.36: 24 70.36 - 87.95: 13 Dihedral angle restraints: 11987 sinusoidal: 5049 harmonic: 6938 Sorted by residual: dihedral pdb=" CA PHE B 10 " pdb=" C PHE B 10 " pdb=" N THR B 11 " pdb=" CA THR B 11 " ideal model delta harmonic sigma weight residual 180.00 157.06 22.94 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA PHE C 10 " pdb=" C PHE C 10 " pdb=" N THR C 11 " pdb=" CA THR C 11 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU j 30 " pdb=" C LEU j 30 " pdb=" N PRO j 31 " pdb=" CA PRO j 31 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 11984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1965 0.031 - 0.061: 704 0.061 - 0.092: 162 0.092 - 0.122: 92 0.122 - 0.153: 19 Chirality restraints: 2942 Sorted by residual: chirality pdb=" CA ILE C 230 " pdb=" N ILE C 230 " pdb=" C ILE C 230 " pdb=" CB ILE C 230 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE A 230 " pdb=" N ILE A 230 " pdb=" C ILE A 230 " pdb=" CB ILE A 230 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE D 230 " pdb=" N ILE D 230 " pdb=" C ILE D 230 " pdb=" CB ILE D 230 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 2939 not shown) Planarity restraints: 3479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 41 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO C 42 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 42 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 42 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU o 30 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO o 31 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO o 31 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO o 31 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 255 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO C 256 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 256 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 256 " 0.019 5.00e-02 4.00e+02 ... (remaining 3476 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 111 2.52 - 3.12: 15046 3.12 - 3.71: 27050 3.71 - 4.31: 36590 4.31 - 4.90: 60372 Nonbonded interactions: 139169 Sorted by model distance: nonbonded pdb=" OG SER b 65 " pdb=" O ASP b 69 " model vdw 1.930 3.040 nonbonded pdb=" OG SER A 440 " pdb=" O GLU C 441 " model vdw 2.113 3.040 nonbonded pdb=" O PHE B 226 " pdb=" OG1 THR B 227 " model vdw 2.131 3.040 nonbonded pdb=" N ASP e 29 " pdb=" OD1 ASP e 29 " model vdw 2.146 3.120 nonbonded pdb=" NZ LYS C 132 " pdb=" O VAL C 248 " model vdw 2.148 3.120 ... (remaining 139164 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 'A' selection = (chain 'C' and (resid 9 through 396 or resid 406 through 448)) } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'a' and resid 10 through 55) selection = (chain 'o' and resid 10 through 55) } ncs_group { reference = (chain 'b' and resid 10 through 65) selection = (chain 'c' and resid 10 through 65) selection = (chain 'd' and resid 10 through 65) selection = (chain 'e' and resid 10 through 65) selection = (chain 'f' and resid 10 through 65) selection = (chain 'g' and resid 10 through 65) selection = (chain 'h' and resid 10 through 65) selection = (chain 'i' and resid 10 through 65) selection = (chain 'j' and resid 10 through 65) selection = (chain 'k' and resid 10 through 65) selection = (chain 'l' and resid 10 through 65) selection = (chain 'm' and resid 10 through 65) selection = (chain 'n' and resid 10 through 65) selection = (chain 'p' and resid 10 through 65) } 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 group one per residue 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: 18.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.050 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.004 0.035 19266 Z= 0.176 Angle : 0.461 4.377 25997 Z= 0.247 Chirality : 0.037 0.153 2942 Planarity : 0.003 0.044 3479 Dihedral : 11.549 87.953 7447 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.59 % Allowed : 2.54 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.92 (0.18), residues: 2336 helix: 0.68 (0.14), residues: 1449 sheet: 0.69 (0.33), residues: 267 loop : 0.78 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 383 TYR 0.011 0.001 TYR A 406 PHE 0.014 0.001 PHE B 10 TRP 0.015 0.001 TRP B 47 HIS 0.003 0.001 HIS C 307 Details of bonding type rmsd covalent geometry : bond 0.00408 (19266) covalent geometry : angle 0.46117 (25997) hydrogen bonds : bond 0.27792 ( 1298) hydrogen bonds : angle 7.47583 ( 3831) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 560 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8672 (mmm160) cc_final: 0.8317 (tpt-90) REVERT: C 187 ARG cc_start: 0.7890 (ttt-90) cc_final: 0.7679 (ttt-90) REVERT: C 339 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7568 (tm-30) REVERT: i 23 THR cc_start: 0.8418 (m) cc_final: 0.8188 (p) REVERT: g 16 SER cc_start: 0.8498 (t) cc_final: 0.8003 (p) REVERT: g 21 ILE cc_start: 0.9012 (mt) cc_final: 0.8811 (mm) REVERT: h 20 GLN cc_start: 0.7937 (mt0) cc_final: 0.7674 (mt0) REVERT: a 34 GLU cc_start: 0.8440 (tp30) cc_final: 0.8052 (tp30) REVERT: b 38 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7740 (mm-30) REVERT: b 47 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7663 (ttm-80) REVERT: B 47 TRP cc_start: 0.7852 (t-100) cc_final: 0.7481 (t-100) REVERT: p 40 GLU cc_start: 0.8929 (tp30) cc_final: 0.8501 (tp30) REVERT: p 64 LEU cc_start: 0.8553 (mp) cc_final: 0.8109 (mm) REVERT: D 71 THR cc_start: 0.9433 (p) cc_final: 0.9168 (t) REVERT: D 282 GLU cc_start: 0.8084 (tp30) cc_final: 0.7829 (tp30) REVERT: m 47 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.7729 (tpp-160) REVERT: n 17 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8545 (mt-10) REVERT: n 45 LEU cc_start: 0.7809 (mt) cc_final: 0.7410 (mt) REVERT: n 48 GLN cc_start: 0.8127 (mt0) cc_final: 0.7490 (mt0) REVERT: n 57 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6949 (tm-30) REVERT: e 44 GLN cc_start: 0.7730 (mt0) cc_final: 0.7266 (mt0) outliers start: 12 outliers final: 6 residues processed: 570 average time/residue: 0.1864 time to fit residues: 145.9880 Evaluate side-chains 441 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 435 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain e residue 29 ASP Chi-restraints excluded: chain f residue 29 ASP Chi-restraints excluded: chain f residue 37 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 96 GLN A 273 GLN A 279 GLN A 304 GLN A 358 HIS C 41 GLN C 422 GLN i 61 GLN c 48 GLN g 20 GLN h 50 GLN h 54 GLN a 44 GLN b 50 GLN b 61 GLN B 300 HIS D 279 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.096359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.076895 restraints weight = 71166.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.076206 restraints weight = 49805.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.076257 restraints weight = 46171.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.076434 restraints weight = 35722.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.076393 restraints weight = 34309.448| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19266 Z= 0.191 Angle : 0.643 9.532 25997 Z= 0.346 Chirality : 0.042 0.205 2942 Planarity : 0.005 0.044 3479 Dihedral : 4.814 48.582 2604 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.39 % Allowed : 9.95 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 1.91 (0.17), residues: 2336 helix: 1.71 (0.13), residues: 1521 sheet: 0.60 (0.33), residues: 264 loop : 0.57 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 59 TYR 0.021 0.002 TYR C 114 PHE 0.016 0.002 PHE B 10 TRP 0.018 0.001 TRP B 47 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00428 (19266) covalent geometry : angle 0.64322 (25997) hydrogen bonds : bond 0.07994 ( 1298) hydrogen bonds : angle 4.46974 ( 3831) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 481 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7902 (mt-10) REVERT: A 335 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7915 (ttpp) REVERT: C 118 LYS cc_start: 0.9252 (tttm) cc_final: 0.8879 (ptmm) REVERT: C 226 PHE cc_start: 0.7705 (m-80) cc_final: 0.7421 (m-80) REVERT: C 339 GLN cc_start: 0.7446 (tm-30) cc_final: 0.7117 (tm-30) REVERT: C 419 LYS cc_start: 0.8567 (tppt) cc_final: 0.8141 (mmmm) REVERT: a 34 GLU cc_start: 0.7660 (tp30) cc_final: 0.7410 (tp30) REVERT: a 38 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8576 (mm-30) REVERT: o 20 GLN cc_start: 0.8418 (tt0) cc_final: 0.8214 (tm-30) REVERT: o 52 LYS cc_start: 0.9166 (ttpp) cc_final: 0.8736 (tmmt) REVERT: p 40 GLU cc_start: 0.8311 (tp30) cc_final: 0.7855 (tp30) REVERT: D 71 THR cc_start: 0.9418 (p) cc_final: 0.9085 (t) REVERT: D 272 ARG cc_start: 0.9130 (tpt170) cc_final: 0.8808 (tpm170) REVERT: D 275 GLN cc_start: 0.8928 (mm110) cc_final: 0.8608 (mm-40) REVERT: D 279 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7921 (mm110) REVERT: D 283 MET cc_start: 0.8532 (tpp) cc_final: 0.8021 (mmt) REVERT: D 285 MET cc_start: 0.8227 (tpp) cc_final: 0.7914 (tpp) REVERT: m 47 ARG cc_start: 0.8372 (tpp-160) cc_final: 0.7501 (tpp-160) REVERT: n 13 LYS cc_start: 0.8258 (ptmm) cc_final: 0.7773 (pptt) REVERT: n 17 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8807 (mt-10) REVERT: n 44 GLN cc_start: 0.8385 (tp-100) cc_final: 0.8110 (tp-100) REVERT: n 45 LEU cc_start: 0.7793 (mt) cc_final: 0.7367 (mt) REVERT: n 54 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7485 (tp-100) REVERT: d 38 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: f 57 GLU cc_start: 0.8108 (tp30) cc_final: 0.7890 (tp30) outliers start: 49 outliers final: 29 residues processed: 505 average time/residue: 0.1933 time to fit residues: 133.4878 Evaluate side-chains 460 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 429 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 63 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 291 ASN Chi-restraints excluded: chain n residue 43 VAL Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain e residue 21 ILE Chi-restraints excluded: chain f residue 37 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 94 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 96 GLN C 38 ASN C 41 GLN C 116 GLN c 44 GLN g 20 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 37 ASN ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.077140 restraints weight = 71705.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.076312 restraints weight = 52279.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.076656 restraints weight = 44949.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.076487 restraints weight = 34274.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.076599 restraints weight = 34581.584| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19266 Z= 0.170 Angle : 0.601 11.092 25997 Z= 0.321 Chirality : 0.041 0.175 2942 Planarity : 0.005 0.056 3479 Dihedral : 4.689 46.567 2599 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.78 % Allowed : 12.78 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.26 (0.17), residues: 2336 helix: 2.06 (0.13), residues: 1520 sheet: 0.46 (0.32), residues: 278 loop : 0.61 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 302 TYR 0.021 0.002 TYR C 114 PHE 0.029 0.002 PHE D 296 TRP 0.014 0.001 TRP A 31 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00381 (19266) covalent geometry : angle 0.60070 (25997) hydrogen bonds : bond 0.06911 ( 1298) hydrogen bonds : angle 4.05962 ( 3831) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 449 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 164 ASP cc_start: 0.7160 (t0) cc_final: 0.6899 (t0) REVERT: C 419 LYS cc_start: 0.8543 (tppt) cc_final: 0.8111 (mmmm) REVERT: g 29 ASP cc_start: 0.8242 (p0) cc_final: 0.7957 (p0) REVERT: h 34 GLU cc_start: 0.7392 (tp30) cc_final: 0.7032 (tp30) REVERT: a 34 GLU cc_start: 0.7497 (tp30) cc_final: 0.7184 (tp30) REVERT: B 47 TRP cc_start: 0.7507 (t-100) cc_final: 0.7057 (t-100) REVERT: o 24 ARG cc_start: 0.8490 (ttm110) cc_final: 0.7963 (ttm110) REVERT: o 52 LYS cc_start: 0.9158 (ttpp) cc_final: 0.8722 (tmmt) REVERT: D 71 THR cc_start: 0.9411 (p) cc_final: 0.9057 (t) REVERT: D 92 ARG cc_start: 0.8750 (mtp85) cc_final: 0.8545 (mtp85) REVERT: D 272 ARG cc_start: 0.9120 (tpt170) cc_final: 0.8893 (tpt170) REVERT: m 24 ARG cc_start: 0.8728 (mmm-85) cc_final: 0.8355 (mmm160) REVERT: m 41 ARG cc_start: 0.8320 (ttp80) cc_final: 0.7765 (ttp80) REVERT: m 47 ARG cc_start: 0.8345 (tpp-160) cc_final: 0.7445 (tpp-160) REVERT: n 13 LYS cc_start: 0.8284 (ptmm) cc_final: 0.7754 (pptt) REVERT: n 17 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8846 (mt-10) REVERT: d 38 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6775 (mp0) outliers start: 57 outliers final: 43 residues processed: 479 average time/residue: 0.2072 time to fit residues: 136.0844 Evaluate side-chains 456 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 412 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain p residue 63 LEU Chi-restraints excluded: chain p residue 64 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain k residue 20 GLN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 21 ILE Chi-restraints excluded: chain f residue 38 GLU Chi-restraints excluded: chain f residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 147 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 187 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN C 41 GLN c 44 GLN g 20 GLN b 50 GLN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 GLN e 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075088 restraints weight = 64267.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.073233 restraints weight = 52647.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.073208 restraints weight = 42854.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.072667 restraints weight = 32488.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.072950 restraints weight = 29475.571| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19266 Z= 0.191 Angle : 0.615 9.408 25997 Z= 0.329 Chirality : 0.041 0.170 2942 Planarity : 0.005 0.063 3479 Dihedral : 4.699 44.815 2597 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.46 % Allowed : 13.71 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.20 (0.17), residues: 2336 helix: 2.06 (0.12), residues: 1522 sheet: 0.44 (0.32), residues: 276 loop : 0.41 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 302 TYR 0.021 0.002 TYR C 114 PHE 0.017 0.002 PHE B 10 TRP 0.016 0.001 TRP C 214 HIS 0.003 0.001 HIS C 300 Details of bonding type rmsd covalent geometry : bond 0.00442 (19266) covalent geometry : angle 0.61523 (25997) hydrogen bonds : bond 0.06932 ( 1298) hydrogen bonds : angle 4.03478 ( 3831) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 423 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8122 (mtm) cc_final: 0.7806 (mtm) REVERT: C 164 ASP cc_start: 0.7125 (t0) cc_final: 0.6704 (t0) REVERT: C 294 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8193 (ttp-110) REVERT: C 419 LYS cc_start: 0.8529 (tppt) cc_final: 0.8116 (mmmm) REVERT: C 424 LYS cc_start: 0.8996 (pptt) cc_final: 0.8707 (pptt) REVERT: c 13 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8461 (tppt) REVERT: g 29 ASP cc_start: 0.8384 (p0) cc_final: 0.8125 (p0) REVERT: h 38 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6568 (mt-10) REVERT: a 34 GLU cc_start: 0.7606 (tp30) cc_final: 0.7306 (tp30) REVERT: B 47 TRP cc_start: 0.7601 (t-100) cc_final: 0.7001 (m-90) REVERT: o 52 LYS cc_start: 0.9183 (ttpp) cc_final: 0.8730 (tmmt) REVERT: p 13 LYS cc_start: 0.8768 (tmmt) cc_final: 0.8100 (tmmt) REVERT: p 47 ARG cc_start: 0.8526 (tpp-160) cc_final: 0.8278 (tpp80) REVERT: D 71 THR cc_start: 0.9441 (p) cc_final: 0.9069 (t) REVERT: D 283 MET cc_start: 0.8632 (tpp) cc_final: 0.7983 (mmt) REVERT: D 305 GLN cc_start: 0.6294 (mm110) cc_final: 0.6049 (mm110) REVERT: m 24 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8298 (mmm160) REVERT: m 41 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7762 (ttp80) REVERT: n 59 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6886 (tmm-80) REVERT: k 47 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7127 (ttp80) REVERT: d 38 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6889 (mp0) outliers start: 71 outliers final: 51 residues processed: 466 average time/residue: 0.1995 time to fit residues: 126.8790 Evaluate side-chains 454 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 400 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain n residue 59 ARG Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain k residue 20 GLN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 30 LEU Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 21 ILE Chi-restraints excluded: chain f residue 29 ASP Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 38 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 49 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 206 optimal weight: 0.8980 chunk 168 optimal weight: 50.0000 chunk 133 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 176 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 67 ASN C 446 GLN c 44 GLN g 20 GLN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 GLN ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN n 54 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.097956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.079486 restraints weight = 70504.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.079646 restraints weight = 43829.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.079790 restraints weight = 36604.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.080030 restraints weight = 26603.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.080133 restraints weight = 22115.344| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19266 Z= 0.174 Angle : 0.609 11.511 25997 Z= 0.322 Chirality : 0.040 0.171 2942 Planarity : 0.004 0.063 3479 Dihedral : 4.626 41.485 2597 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.56 % Allowed : 15.17 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.32 (0.17), residues: 2336 helix: 2.20 (0.13), residues: 1521 sheet: 0.37 (0.32), residues: 275 loop : 0.38 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG h 24 TYR 0.022 0.002 TYR C 114 PHE 0.015 0.002 PHE B 10 TRP 0.014 0.001 TRP C 214 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00397 (19266) covalent geometry : angle 0.60909 (25997) hydrogen bonds : bond 0.06593 ( 1298) hydrogen bonds : angle 3.94587 ( 3831) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 411 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 170 ILE cc_start: 0.8572 (mm) cc_final: 0.8333 (mm) REVERT: C 419 LYS cc_start: 0.8450 (tppt) cc_final: 0.8042 (mmmm) REVERT: C 424 LYS cc_start: 0.8896 (pptt) cc_final: 0.8552 (pptt) REVERT: C 428 MET cc_start: 0.7921 (mmm) cc_final: 0.7700 (tpt) REVERT: i 30 LEU cc_start: 0.8152 (tp) cc_final: 0.7867 (tp) REVERT: c 13 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8343 (tppt) REVERT: g 29 ASP cc_start: 0.8307 (p0) cc_final: 0.8009 (p0) REVERT: h 34 GLU cc_start: 0.7513 (tp30) cc_final: 0.6900 (tp30) REVERT: h 38 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6566 (mt-10) REVERT: a 34 GLU cc_start: 0.7509 (tp30) cc_final: 0.7203 (tp30) REVERT: B 47 TRP cc_start: 0.7587 (t-100) cc_final: 0.7119 (m-90) REVERT: o 20 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7584 (tm-30) REVERT: o 52 LYS cc_start: 0.9184 (ttpp) cc_final: 0.8771 (tmmt) REVERT: p 13 LYS cc_start: 0.8988 (tmmt) cc_final: 0.8647 (tmmt) REVERT: D 71 THR cc_start: 0.9449 (p) cc_final: 0.9060 (t) REVERT: D 283 MET cc_start: 0.8572 (tpp) cc_final: 0.8107 (mmt) REVERT: m 24 ARG cc_start: 0.8723 (mmm-85) cc_final: 0.8277 (mmm160) REVERT: m 41 ARG cc_start: 0.8519 (ttp80) cc_final: 0.8159 (ttp80) REVERT: k 47 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7137 (ttp80) REVERT: d 38 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: e 21 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8513 (tt) outliers start: 73 outliers final: 58 residues processed: 451 average time/residue: 0.1962 time to fit residues: 122.6121 Evaluate side-chains 465 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 404 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 20 GLN Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 55 GLN Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain n residue 53 LEU Chi-restraints excluded: chain n residue 59 ARG Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain k residue 20 GLN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain k residue 36 LEU Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 21 ILE Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain f residue 29 ASP Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 38 GLU Chi-restraints excluded: chain f residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 214 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN c 44 GLN c 48 GLN g 20 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN n 54 GLN ** n 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.097819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.074464 restraints weight = 58529.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.072438 restraints weight = 47533.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.072407 restraints weight = 38476.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.072270 restraints weight = 30995.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.072270 restraints weight = 29559.879| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19266 Z= 0.189 Angle : 0.636 13.717 25997 Z= 0.336 Chirality : 0.041 0.206 2942 Planarity : 0.004 0.061 3479 Dihedral : 4.650 41.979 2597 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.76 % Allowed : 16.49 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.26 (0.17), residues: 2336 helix: 2.15 (0.13), residues: 1522 sheet: 0.39 (0.32), residues: 273 loop : 0.32 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 302 TYR 0.021 0.002 TYR C 114 PHE 0.017 0.002 PHE B 10 TRP 0.015 0.001 TRP C 214 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00441 (19266) covalent geometry : angle 0.63574 (25997) hydrogen bonds : bond 0.06717 ( 1298) hydrogen bonds : angle 3.97322 ( 3831) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 407 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 170 ILE cc_start: 0.8643 (mm) cc_final: 0.8410 (mm) REVERT: C 419 LYS cc_start: 0.8418 (tppt) cc_final: 0.7999 (mmmm) REVERT: C 424 LYS cc_start: 0.8996 (pptt) cc_final: 0.8642 (pptt) REVERT: C 428 MET cc_start: 0.8129 (mmm) cc_final: 0.7802 (tpt) REVERT: h 13 LYS cc_start: 0.8643 (ttpp) cc_final: 0.8268 (pttm) REVERT: h 34 GLU cc_start: 0.7793 (tp30) cc_final: 0.7036 (tp30) REVERT: h 38 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6727 (mt-10) REVERT: a 34 GLU cc_start: 0.7608 (tp30) cc_final: 0.7261 (tp30) REVERT: o 63 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5739 (mp) REVERT: p 41 ARG cc_start: 0.6960 (mmm160) cc_final: 0.6757 (mmm160) REVERT: D 71 THR cc_start: 0.9432 (p) cc_final: 0.9023 (t) REVERT: D 272 ARG cc_start: 0.9184 (tpt170) cc_final: 0.8779 (mmm160) REVERT: D 294 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8591 (ttp80) REVERT: m 24 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8225 (mmm160) REVERT: m 33 GLU cc_start: 0.8138 (pm20) cc_final: 0.7928 (pm20) REVERT: m 41 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7978 (ttp80) REVERT: n 59 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6776 (tmm-80) REVERT: k 47 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7111 (ttp80) REVERT: d 34 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7242 (mm-30) REVERT: d 38 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: e 36 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8397 (tt) REVERT: f 24 ARG cc_start: 0.8007 (mtp-110) cc_final: 0.7771 (ttm-80) outliers start: 77 outliers final: 63 residues processed: 451 average time/residue: 0.1912 time to fit residues: 119.7143 Evaluate side-chains 462 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 394 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain h residue 58 GLN Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain b residue 36 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain o residue 63 LEU Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 17 GLU Chi-restraints excluded: chain p residue 20 GLN Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 53 LEU Chi-restraints excluded: chain p residue 55 GLN Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain n residue 59 ARG Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain k residue 20 GLN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 30 LEU Chi-restraints excluded: chain k residue 34 GLU Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 45 LEU Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 21 ILE Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain e residue 54 GLN Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain f residue 29 ASP Chi-restraints excluded: chain f residue 37 ASN Chi-restraints excluded: chain f residue 38 GLU Chi-restraints excluded: chain f residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 49 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 116 optimal weight: 0.0060 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 217 optimal weight: 0.0040 chunk 225 optimal weight: 0.1980 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 217 ASN c 44 GLN g 20 GLN b 50 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN n 54 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.073525 restraints weight = 58816.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.072872 restraints weight = 44265.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.072624 restraints weight = 31039.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.072576 restraints weight = 23972.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.072526 restraints weight = 24698.029| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19266 Z= 0.144 Angle : 0.613 12.886 25997 Z= 0.319 Chirality : 0.039 0.199 2942 Planarity : 0.004 0.058 3479 Dihedral : 4.400 35.418 2597 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.07 % Allowed : 18.44 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.59 (0.17), residues: 2336 helix: 2.45 (0.13), residues: 1515 sheet: 0.50 (0.33), residues: 263 loop : 0.32 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 302 TYR 0.019 0.001 TYR C 114 PHE 0.011 0.001 PHE C 296 TRP 0.013 0.001 TRP C 214 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00319 (19266) covalent geometry : angle 0.61315 (25997) hydrogen bonds : bond 0.05766 ( 1298) hydrogen bonds : angle 3.73523 ( 3831) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 425 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.7523 (tpp80) cc_final: 0.7087 (mpp80) REVERT: C 170 ILE cc_start: 0.8558 (mm) cc_final: 0.8316 (mm) REVERT: C 424 LYS cc_start: 0.8905 (pptt) cc_final: 0.8549 (pptt) REVERT: C 428 MET cc_start: 0.7865 (mmm) cc_final: 0.7596 (tpt) REVERT: i 58 GLN cc_start: 0.8506 (tp40) cc_final: 0.8255 (tp40) REVERT: g 29 ASP cc_start: 0.8354 (p0) cc_final: 0.8108 (p0) REVERT: h 13 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8369 (pttm) REVERT: h 34 GLU cc_start: 0.7460 (tp30) cc_final: 0.6922 (tp30) REVERT: h 38 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6733 (mt-10) REVERT: a 24 ARG cc_start: 0.8728 (tpp80) cc_final: 0.8351 (ttm110) REVERT: a 34 GLU cc_start: 0.7478 (tp30) cc_final: 0.7135 (tp30) REVERT: o 34 GLU cc_start: 0.8188 (mp0) cc_final: 0.7908 (mp0) REVERT: o 52 LYS cc_start: 0.9201 (ttpp) cc_final: 0.8773 (tmmt) REVERT: o 63 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5781 (mp) REVERT: p 26 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7489 (mt-10) REVERT: p 37 ASN cc_start: 0.8173 (p0) cc_final: 0.7383 (p0) REVERT: p 47 ARG cc_start: 0.8903 (tpp80) cc_final: 0.8702 (tpp-160) REVERT: D 71 THR cc_start: 0.9431 (p) cc_final: 0.9024 (t) REVERT: D 283 MET cc_start: 0.8461 (tpp) cc_final: 0.8183 (mmm) REVERT: D 294 ARG cc_start: 0.8721 (ttp80) cc_final: 0.8499 (ttp80) REVERT: m 24 ARG cc_start: 0.8397 (mmm-85) cc_final: 0.7946 (mmm160) REVERT: m 41 ARG cc_start: 0.7710 (ttp80) cc_final: 0.7496 (ttp80) REVERT: k 47 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7105 (ttp80) REVERT: l 19 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6857 (mt-10) REVERT: d 34 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7132 (mm-30) REVERT: d 38 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: e 21 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8523 (tt) REVERT: e 36 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8222 (tt) REVERT: f 24 ARG cc_start: 0.7969 (mtp-110) cc_final: 0.7711 (ttm-80) outliers start: 63 outliers final: 44 residues processed: 465 average time/residue: 0.2012 time to fit residues: 129.2767 Evaluate side-chains 452 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 402 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain c residue 30 LEU Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain o residue 63 LEU Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 17 GLU Chi-restraints excluded: chain p residue 53 LEU Chi-restraints excluded: chain p residue 55 GLN Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain n residue 54 GLN Chi-restraints excluded: chain n residue 59 ARG Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain k residue 20 GLN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 19 GLU Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 21 ILE Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 194 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 218 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 221 optimal weight: 0.4980 chunk 203 optimal weight: 0.0670 chunk 177 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 446 GLN c 44 GLN g 20 GLN b 67 ASN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN n 54 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.098967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077099 restraints weight = 58900.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.074469 restraints weight = 45883.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.073606 restraints weight = 38224.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073116 restraints weight = 33397.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073427 restraints weight = 28804.360| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19266 Z= 0.148 Angle : 0.636 13.027 25997 Z= 0.329 Chirality : 0.040 0.192 2942 Planarity : 0.004 0.056 3479 Dihedral : 4.263 31.565 2595 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.49 % Allowed : 19.41 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.62 (0.17), residues: 2336 helix: 2.49 (0.13), residues: 1515 sheet: 0.50 (0.33), residues: 263 loop : 0.31 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 432 TYR 0.019 0.001 TYR C 114 PHE 0.012 0.001 PHE A 39 TRP 0.023 0.001 TRP A 47 HIS 0.006 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00333 (19266) covalent geometry : angle 0.63591 (25997) hydrogen bonds : bond 0.05696 ( 1298) hydrogen bonds : angle 3.71476 ( 3831) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 413 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.7532 (tpp80) cc_final: 0.7109 (mpp80) REVERT: C 170 ILE cc_start: 0.8557 (mm) cc_final: 0.8310 (mm) REVERT: C 419 LYS cc_start: 0.8335 (tppt) cc_final: 0.7939 (mmmm) REVERT: C 424 LYS cc_start: 0.8902 (pptt) cc_final: 0.8569 (pptt) REVERT: i 58 GLN cc_start: 0.8538 (tp40) cc_final: 0.8271 (tp40) REVERT: g 29 ASP cc_start: 0.8393 (p0) cc_final: 0.8167 (p0) REVERT: h 34 GLU cc_start: 0.7513 (tp30) cc_final: 0.6984 (tp30) REVERT: h 38 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6743 (mt-10) REVERT: a 24 ARG cc_start: 0.8712 (tpp80) cc_final: 0.8376 (ttm110) REVERT: b 12 GLU cc_start: 0.8454 (mp0) cc_final: 0.8193 (mp0) REVERT: b 38 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7306 (mm-30) REVERT: o 20 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7768 (tm-30) REVERT: o 52 LYS cc_start: 0.9192 (ttpp) cc_final: 0.8738 (tmmt) REVERT: o 63 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5697 (mp) REVERT: D 71 THR cc_start: 0.9412 (p) cc_final: 0.9000 (t) REVERT: D 283 MET cc_start: 0.8682 (tpp) cc_final: 0.7931 (mmt) REVERT: D 294 ARG cc_start: 0.8944 (ttp80) cc_final: 0.8615 (ttp80) REVERT: m 24 ARG cc_start: 0.8697 (mmm-85) cc_final: 0.8182 (mmm160) REVERT: m 41 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7853 (ttp80) REVERT: j 57 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6805 (mm-30) REVERT: k 47 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7071 (ttp80) REVERT: l 19 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: e 21 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8482 (tt) REVERT: e 36 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8142 (tt) outliers start: 51 outliers final: 41 residues processed: 444 average time/residue: 0.2089 time to fit residues: 128.2645 Evaluate side-chains 449 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 403 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain c residue 30 LEU Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain o residue 63 LEU Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 17 GLU Chi-restraints excluded: chain p residue 53 LEU Chi-restraints excluded: chain p residue 55 GLN Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain n residue 54 GLN Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain k residue 20 GLN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain l residue 19 GLU Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 21 ILE Chi-restraints excluded: chain e residue 36 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 56 optimal weight: 0.4980 chunk 221 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 153 optimal weight: 0.4980 chunk 132 optimal weight: 0.5980 chunk 133 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 179 optimal weight: 40.0000 chunk 213 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN c 44 GLN c 54 GLN g 20 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN n 54 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.075593 restraints weight = 59400.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074769 restraints weight = 42346.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.074756 restraints weight = 34227.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.074973 restraints weight = 27574.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.074826 restraints weight = 24182.791| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19266 Z= 0.159 Angle : 0.664 13.252 25997 Z= 0.343 Chirality : 0.040 0.189 2942 Planarity : 0.004 0.055 3479 Dihedral : 4.235 24.052 2593 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.83 % Allowed : 19.46 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.57 (0.17), residues: 2336 helix: 2.46 (0.13), residues: 1513 sheet: 0.49 (0.33), residues: 263 loop : 0.24 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG b 41 TYR 0.019 0.001 TYR A 95 PHE 0.016 0.001 PHE A 39 TRP 0.032 0.001 TRP A 47 HIS 0.009 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00364 (19266) covalent geometry : angle 0.66442 (25997) hydrogen bonds : bond 0.05835 ( 1298) hydrogen bonds : angle 3.75320 ( 3831) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 408 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.7531 (tpp80) cc_final: 0.7134 (mpp80) REVERT: C 419 LYS cc_start: 0.8415 (tppt) cc_final: 0.7998 (mmmm) REVERT: C 424 LYS cc_start: 0.8996 (pptt) cc_final: 0.8629 (pptt) REVERT: i 58 GLN cc_start: 0.8576 (tp40) cc_final: 0.8322 (tp40) REVERT: g 29 ASP cc_start: 0.8409 (p0) cc_final: 0.8167 (p0) REVERT: h 13 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8295 (pttm) REVERT: h 38 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6494 (mt-10) REVERT: a 24 ARG cc_start: 0.8703 (tpp80) cc_final: 0.8397 (ttm110) REVERT: b 38 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7258 (mm-30) REVERT: B 301 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.8062 (t-90) REVERT: o 20 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7760 (tm-30) REVERT: o 63 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5640 (mp) REVERT: D 71 THR cc_start: 0.9425 (p) cc_final: 0.9010 (t) REVERT: D 282 GLU cc_start: 0.8108 (tp30) cc_final: 0.7565 (tm-30) REVERT: D 283 MET cc_start: 0.8566 (tpp) cc_final: 0.8064 (mmt) REVERT: D 294 ARG cc_start: 0.8912 (ttp80) cc_final: 0.8686 (ttp80) REVERT: m 24 ARG cc_start: 0.8591 (mmm-85) cc_final: 0.8264 (mmm160) REVERT: m 41 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7673 (ttp80) REVERT: k 47 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7072 (ttp80) REVERT: e 36 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8224 (tt) outliers start: 58 outliers final: 46 residues processed: 443 average time/residue: 0.2004 time to fit residues: 122.3541 Evaluate side-chains 448 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 398 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 301 HIS Chi-restraints excluded: chain o residue 63 LEU Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 53 LEU Chi-restraints excluded: chain p residue 55 GLN Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain n residue 54 GLN Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain k residue 20 GLN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 21 ILE Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 132 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 180 optimal weight: 30.0000 chunk 166 optimal weight: 10.0000 chunk 209 optimal weight: 0.5980 chunk 191 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 210 optimal weight: 0.0470 chunk 82 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 446 GLN c 44 GLN g 20 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN n 54 GLN ** n 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.099267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.075985 restraints weight = 59251.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.074757 restraints weight = 41640.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.074984 restraints weight = 28334.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.075532 restraints weight = 22954.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.075438 restraints weight = 20174.824| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19266 Z= 0.163 Angle : 0.690 12.926 25997 Z= 0.355 Chirality : 0.041 0.310 2942 Planarity : 0.005 0.052 3479 Dihedral : 4.280 24.215 2593 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.49 % Allowed : 20.00 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.51 (0.17), residues: 2336 helix: 2.41 (0.13), residues: 1512 sheet: 0.48 (0.33), residues: 263 loop : 0.22 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 68 TYR 0.019 0.001 TYR A 95 PHE 0.013 0.001 PHE B 10 TRP 0.030 0.001 TRP A 47 HIS 0.008 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00376 (19266) covalent geometry : angle 0.68956 (25997) hydrogen bonds : bond 0.05913 ( 1298) hydrogen bonds : angle 3.78772 ( 3831) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 405 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.7518 (tpp80) cc_final: 0.7117 (mpp80) REVERT: C 419 LYS cc_start: 0.8402 (tppt) cc_final: 0.7988 (mmmm) REVERT: C 424 LYS cc_start: 0.8949 (pptt) cc_final: 0.8614 (pptt) REVERT: i 58 GLN cc_start: 0.8526 (tp40) cc_final: 0.8265 (tp40) REVERT: g 29 ASP cc_start: 0.8390 (p0) cc_final: 0.8139 (p0) REVERT: h 13 LYS cc_start: 0.8633 (ttpp) cc_final: 0.8298 (pttm) REVERT: h 30 LEU cc_start: 0.8682 (mt) cc_final: 0.8340 (mt) REVERT: h 34 GLU cc_start: 0.6926 (tm-30) cc_final: 0.5611 (tm-30) REVERT: a 24 ARG cc_start: 0.8717 (tpp80) cc_final: 0.8415 (ttm110) REVERT: o 20 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7757 (tm-30) REVERT: o 63 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5609 (mp) REVERT: D 71 THR cc_start: 0.9423 (p) cc_final: 0.9000 (t) REVERT: D 282 GLU cc_start: 0.8117 (tp30) cc_final: 0.7581 (tm-30) REVERT: D 283 MET cc_start: 0.8578 (tpp) cc_final: 0.8075 (mmt) REVERT: D 294 ARG cc_start: 0.8929 (ttp80) cc_final: 0.8702 (ttp80) REVERT: m 24 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8305 (mmm160) REVERT: m 41 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7666 (ttp80) REVERT: k 47 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7059 (ttp80) REVERT: e 36 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8226 (tt) outliers start: 51 outliers final: 45 residues processed: 436 average time/residue: 0.1856 time to fit residues: 112.0469 Evaluate side-chains 446 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 398 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 437 TRP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain o residue 63 LEU Chi-restraints excluded: chain p residue 15 LEU Chi-restraints excluded: chain p residue 20 GLN Chi-restraints excluded: chain p residue 53 LEU Chi-restraints excluded: chain p residue 55 GLN Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain n residue 54 GLN Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 43 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain k residue 20 GLN Chi-restraints excluded: chain k residue 21 ILE Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 62 ILE Chi-restraints excluded: chain e residue 21 ILE Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 43 VAL Chi-restraints excluded: chain f residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 40 optimal weight: 0.0670 chunk 158 optimal weight: 1.9990 chunk 29 optimal weight: 0.0060 chunk 16 optimal weight: 0.0670 chunk 61 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 180 optimal weight: 40.0000 chunk 204 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 171 optimal weight: 6.9990 overall best weight: 0.1672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 309 GLN c 44 GLN c 48 GLN c 54 GLN g 20 GLN ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN n 54 GLN ** n 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.100787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075742 restraints weight = 59345.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.074243 restraints weight = 41389.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.074456 restraints weight = 27439.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.074462 restraints weight = 21152.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.074462 restraints weight = 21004.854| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19266 Z= 0.138 Angle : 0.668 12.787 25997 Z= 0.342 Chirality : 0.039 0.201 2942 Planarity : 0.004 0.051 3479 Dihedral : 4.056 22.329 2593 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.76 % Allowed : 20.63 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 2.78 (0.17), residues: 2336 helix: 2.67 (0.13), residues: 1511 sheet: 0.34 (0.32), residues: 279 loop : 0.32 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 68 TYR 0.018 0.001 TYR A 95 PHE 0.012 0.001 PHE C 226 TRP 0.018 0.001 TRP A 47 HIS 0.006 0.000 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00306 (19266) covalent geometry : angle 0.66814 (25997) hydrogen bonds : bond 0.04847 ( 1298) hydrogen bonds : angle 3.60705 ( 3831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4215.55 seconds wall clock time: 73 minutes 6.91 seconds (4386.91 seconds total)