Starting phenix.real_space_refine on Mon Jun 16 15:06:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txr_41704/06_2025/8txr_41704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txr_41704/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8txr_41704/06_2025/8txr_41704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txr_41704/06_2025/8txr_41704.map" model { file = "/net/cci-nas-00/data/ceres_data/8txr_41704/06_2025/8txr_41704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txr_41704/06_2025/8txr_41704.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.01, per 1000 atoms: 0.74 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: 5.19 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.01 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: 6.80 Time building geometry restraints manager: 6.13 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: 11.390 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: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 48.800 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.110 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.310 ------------------------------------------------------------------------------- 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 : 3.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP B 47 HIS 0.003 0.001 HIS C 307 PHE 0.014 0.001 PHE B 10 TYR 0.011 0.001 TYR A 406 ARG 0.003 0.000 ARG A 383 Details of bonding type rmsd hydrogen bonds : bond 0.27792 ( 1298) hydrogen bonds : angle 7.47583 ( 3831) covalent geometry : bond 0.00408 (19266) covalent geometry : angle 0.46117 (25997) *********************** 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 : 2.179 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 14 ARG cc_start: 0.8672 (mmm160) cc_final: 0.8315 (tpt-90) REVERT: C 187 ARG cc_start: 0.7890 (ttt-90) cc_final: 0.7677 (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: 0.8187 (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: 0.7668 (mt0) REVERT: a 34 GLU cc_start: 0.8440 (tp30) cc_final: 0.8051 (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: 0.7664 (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: 0.8498 (tp30) 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: 0.7833 (tp30) REVERT: m 47 ARG cc_start: 0.8405 (tpp-160) cc_final: 0.7681 (tpp-160) REVERT: n 17 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8529 (mt-10) REVERT: n 45 LEU cc_start: 0.7809 (mt) cc_final: 0.7390 (mt) REVERT: n 48 GLN cc_start: 0.8127 (mt0) cc_final: 0.7491 (mt0) REVERT: n 57 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6948 (tm-30) REVERT: e 44 GLN cc_start: 0.7730 (mt0) cc_final: 0.7264 (mt0) outliers start: 12 outliers final: 6 residues processed: 570 average time/residue: 0.4265 time to fit residues: 332.4811 Evaluate side-chains 443 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 437 time to evaluate : 2.928 ------------------------------------------------------------------------------- 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 192 optimal weight: 6.9990 chunk 172 optimal weight: 30.0000 chunk 95 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 178 optimal weight: 40.0000 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 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 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.099747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.077263 restraints weight = 66438.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.076468 restraints weight = 45001.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.074927 restraints weight = 40883.693| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19266 Z= 0.194 Angle : 0.648 9.124 25997 Z= 0.350 Chirality : 0.042 0.184 2942 Planarity : 0.005 0.044 3479 Dihedral : 4.822 48.256 2604 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.44 % Allowed : 9.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.17), residues: 2336 helix: 1.70 (0.12), residues: 1519 sheet: 0.64 (0.33), residues: 262 loop : 0.59 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 47 HIS 0.005 0.001 HIS B 140 PHE 0.016 0.002 PHE B 10 TYR 0.022 0.002 TYR C 114 ARG 0.015 0.001 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.07870 ( 1298) hydrogen bonds : angle 4.46721 ( 3831) covalent geometry : bond 0.00435 (19266) covalent geometry : angle 0.64754 (25997) *********************** 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 532 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 482 time to evaluate : 2.120 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: A 62 MET cc_start: 0.5519 (ttp) cc_final: 0.5260 (ttt) REVERT: A 90 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7922 (mt-10) REVERT: A 335 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7905 (ttpp) REVERT: C 118 LYS cc_start: 0.9196 (tttm) cc_final: 0.8856 (ptmm) REVERT: C 226 PHE cc_start: 0.7695 (m-80) cc_final: 0.7386 (m-80) REVERT: C 339 GLN cc_start: 0.7467 (tm-30) cc_final: 0.7103 (tm-30) REVERT: C 419 LYS cc_start: 0.8426 (tppt) cc_final: 0.8018 (mmmm) REVERT: a 34 GLU cc_start: 0.7705 (tp30) cc_final: 0.7443 (tp30) REVERT: a 38 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8592 (mm-30) REVERT: B 47 TRP cc_start: 0.7801 (t-100) cc_final: 0.7574 (t-100) REVERT: o 20 GLN cc_start: 0.8437 (tt0) cc_final: 0.8203 (tm-30) REVERT: o 52 LYS cc_start: 0.9154 (ttpp) cc_final: 0.8716 (tmmt) REVERT: p 40 GLU cc_start: 0.8191 (tp30) cc_final: 0.7822 (tp30) REVERT: D 71 THR cc_start: 0.9430 (p) cc_final: 0.9097 (t) REVERT: D 272 ARG cc_start: 0.9010 (tpt170) cc_final: 0.8748 (tpm170) REVERT: D 275 GLN cc_start: 0.8945 (mm110) cc_final: 0.8535 (mm-40) REVERT: D 279 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7768 (mm110) REVERT: D 283 MET cc_start: 0.8338 (tpp) cc_final: 0.7886 (mmt) REVERT: m 47 ARG cc_start: 0.8288 (tpp-160) cc_final: 0.7610 (tpp-160) REVERT: n 13 LYS cc_start: 0.8036 (ptmm) cc_final: 0.7786 (pptt) REVERT: n 17 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8815 (mt-10) REVERT: n 45 LEU cc_start: 0.7780 (mt) cc_final: 0.7348 (mt) REVERT: n 54 GLN cc_start: 0.7975 (tp-100) cc_final: 0.7586 (tp-100) REVERT: n 58 GLN cc_start: 0.8813 (tp40) cc_final: 0.8547 (pp30) REVERT: d 38 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: f 21 ILE cc_start: 0.8052 (mt) cc_final: 0.7696 (mm) outliers start: 50 outliers final: 28 residues processed: 506 average time/residue: 0.4171 time to fit residues: 288.1228 Evaluate side-chains 461 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 431 time to evaluate : 2.155 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 188 optimal weight: 0.5980 chunk 198 optimal weight: 0.4980 chunk 147 optimal weight: 0.0570 chunk 189 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 156 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 44 GLN g 20 GLN b 50 GLN b 61 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.097012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.077537 restraints weight = 71029.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.076486 restraints weight = 53921.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076558 restraints weight = 50618.045| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19266 Z= 0.150 Angle : 0.569 6.771 25997 Z= 0.305 Chirality : 0.040 0.174 2942 Planarity : 0.004 0.054 3479 Dihedral : 4.561 43.829 2599 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.34 % Allowed : 12.63 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.17), residues: 2336 helix: 2.24 (0.13), residues: 1520 sheet: 0.55 (0.32), residues: 275 loop : 0.61 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 47 HIS 0.003 0.001 HIS B 140 PHE 0.031 0.002 PHE D 296 TYR 0.020 0.001 TYR C 114 ARG 0.009 0.001 ARG n 59 Details of bonding type rmsd hydrogen bonds : bond 0.06449 ( 1298) hydrogen bonds : angle 3.93715 ( 3831) covalent geometry : bond 0.00324 (19266) covalent geometry : angle 0.56862 (25997) *********************** 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 502 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 454 time to evaluate : 2.274 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: C 62 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6495 (ttt) REVERT: C 164 ASP cc_start: 0.6968 (t0) cc_final: 0.6720 (t0) REVERT: C 419 LYS cc_start: 0.8643 (tppt) cc_final: 0.8198 (mmmm) REVERT: c 40 GLU cc_start: 0.6251 (tm-30) cc_final: 0.6049 (tm-30) REVERT: g 29 ASP cc_start: 0.8228 (p0) cc_final: 0.7967 (p0) REVERT: h 34 GLU cc_start: 0.7383 (tp30) cc_final: 0.6579 (tp30) REVERT: a 34 GLU cc_start: 0.7435 (tp30) cc_final: 0.7056 (tp30) REVERT: b 50 GLN cc_start: 0.7922 (tp40) cc_final: 0.7684 (tp-100) REVERT: B 179 ASP cc_start: 0.7675 (p0) cc_final: 0.7444 (p0) REVERT: o 24 ARG cc_start: 0.8451 (ttm110) cc_final: 0.7955 (ttm110) REVERT: o 52 LYS cc_start: 0.9179 (ttpp) cc_final: 0.8740 (tmmt) REVERT: D 71 THR cc_start: 0.9387 (p) cc_final: 0.9033 (t) REVERT: D 272 ARG cc_start: 0.9149 (tpt170) cc_final: 0.8947 (tpt170) REVERT: D 283 MET cc_start: 0.8472 (tpp) cc_final: 0.8231 (mmt) REVERT: D 305 GLN cc_start: 0.6552 (mm110) cc_final: 0.6145 (mp10) REVERT: m 24 ARG cc_start: 0.8736 (mmm-85) cc_final: 0.8350 (mmm160) REVERT: m 41 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8128 (ttp80) REVERT: m 47 ARG cc_start: 0.8171 (tpp-160) cc_final: 0.7378 (tpp-160) REVERT: n 13 LYS cc_start: 0.8193 (ptmm) cc_final: 0.7747 (pptt) REVERT: n 17 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8866 (mt-10) REVERT: n 61 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8783 (tp-100) REVERT: d 38 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: e 21 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8559 (tt) outliers start: 48 outliers final: 35 residues processed: 480 average time/residue: 0.4291 time to fit residues: 281.3864 Evaluate side-chains 458 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 420 time to evaluate : 2.194 ------------------------------------------------------------------------------- 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 62 MET 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 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 48 GLN 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 p residue 15 LEU 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 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 65 SER 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 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 114 optimal weight: 0.9980 chunk 205 optimal weight: 0.5980 chunk 70 optimal weight: 0.0370 chunk 224 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 106 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 44 GLN g 20 GLN b 67 ASN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 GLN m 50 GLN ** n 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 GLN e 44 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.099397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.077357 restraints weight = 64689.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.075951 restraints weight = 52794.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.075689 restraints weight = 41126.691| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19266 Z= 0.145 Angle : 0.562 7.043 25997 Z= 0.300 Chirality : 0.039 0.173 2942 Planarity : 0.004 0.060 3479 Dihedral : 4.389 38.632 2597 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.93 % Allowed : 13.46 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.17), residues: 2336 helix: 2.43 (0.13), residues: 1515 sheet: 0.62 (0.33), residues: 263 loop : 0.46 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 47 HIS 0.005 0.001 HIS B 140 PHE 0.013 0.001 PHE D 296 TYR 0.018 0.001 TYR C 114 ARG 0.008 0.001 ARG B 73 Details of bonding type rmsd hydrogen bonds : bond 0.06000 ( 1298) hydrogen bonds : angle 3.80079 ( 3831) covalent geometry : bond 0.00318 (19266) covalent geometry : angle 0.56223 (25997) *********************** 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 506 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 446 time to evaluate : 2.399 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: 0.7578 (tpp80) cc_final: 0.7008 (mpp80) REVERT: C 62 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6455 (ttt) REVERT: C 419 LYS cc_start: 0.8614 (tppt) cc_final: 0.8147 (mmmm) REVERT: c 40 GLU cc_start: 0.6069 (tm-30) cc_final: 0.5838 (tm-30) REVERT: g 29 ASP cc_start: 0.8268 (p0) cc_final: 0.8049 (p0) REVERT: h 38 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6332 (mt-10) REVERT: a 34 GLU cc_start: 0.7486 (tp30) cc_final: 0.7184 (tp30) REVERT: B 47 TRP cc_start: 0.8210 (t-100) cc_final: 0.7765 (t-100) REVERT: B 179 ASP cc_start: 0.7655 (p0) cc_final: 0.7357 (p0) REVERT: o 52 LYS cc_start: 0.9168 (ttpp) cc_final: 0.8709 (tmmt) REVERT: p 13 LYS cc_start: 0.8684 (tmmt) cc_final: 0.8124 (tmmt) REVERT: p 17 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8017 (mp0) REVERT: p 47 ARG cc_start: 0.8516 (tpp-160) cc_final: 0.8262 (tpp80) REVERT: D 71 THR cc_start: 0.9438 (p) cc_final: 0.9068 (t) REVERT: m 24 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8333 (mmm160) REVERT: m 41 ARG cc_start: 0.8319 (ttp80) cc_final: 0.8055 (ttp80) REVERT: n 59 ARG cc_start: 0.7039 (ttp80) cc_final: 0.6793 (tmt170) REVERT: n 61 GLN cc_start: 0.9104 (tp-100) cc_final: 0.8864 (tp-100) REVERT: k 47 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7100 (ttp80) REVERT: d 34 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7072 (mm-30) REVERT: d 38 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: e 21 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8528 (tt) outliers start: 60 outliers final: 41 residues processed: 480 average time/residue: 0.4332 time to fit residues: 284.6795 Evaluate side-chains 450 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 405 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS 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 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 62 MET 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 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 30 LEU Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 48 GLN Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain a residue 53 LEU 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 p residue 15 LEU Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 291 ASN Chi-restraints excluded: chain j residue 30 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 30 LEU Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 59 optimal weight: 0.5980 chunk 184 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 chunk 210 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 0.1980 chunk 68 optimal weight: 0.5980 chunk 212 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 i 61 GLN c 44 GLN g 20 GLN b 50 GLN ** p 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 GLN e 44 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.098859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.076466 restraints weight = 65101.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.074995 restraints weight = 54285.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.074745 restraints weight = 41116.898| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19266 Z= 0.154 Angle : 0.583 11.922 25997 Z= 0.307 Chirality : 0.040 0.170 2942 Planarity : 0.004 0.061 3479 Dihedral : 4.383 35.089 2597 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.46 % Allowed : 14.39 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.17), residues: 2336 helix: 2.42 (0.13), residues: 1512 sheet: 0.61 (0.32), residues: 264 loop : 0.45 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 47 HIS 0.005 0.001 HIS B 140 PHE 0.025 0.001 PHE C 226 TYR 0.017 0.001 TYR C 114 ARG 0.011 0.001 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.06079 ( 1298) hydrogen bonds : angle 3.80281 ( 3831) covalent geometry : bond 0.00348 (19266) covalent geometry : angle 0.58324 (25997) *********************** 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: 71 poor density : 413 time to evaluate : 2.276 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: 0.7515 (tpp80) cc_final: 0.7011 (mpp80) REVERT: C 62 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6452 (ttt) REVERT: C 419 LYS cc_start: 0.8559 (tppt) cc_final: 0.8099 (mmmm) REVERT: g 29 ASP cc_start: 0.8265 (p0) cc_final: 0.8033 (p0) REVERT: a 24 ARG cc_start: 0.8686 (tpp80) cc_final: 0.8327 (ttm110) REVERT: a 34 GLU cc_start: 0.7497 (tp30) cc_final: 0.7169 (tp30) REVERT: B 73 ARG cc_start: 0.8000 (mmp-170) cc_final: 0.7796 (mmm160) REVERT: o 52 LYS cc_start: 0.9168 (ttpp) cc_final: 0.8722 (tmmt) REVERT: p 13 LYS cc_start: 0.8969 (tmmt) cc_final: 0.8511 (tmmt) REVERT: D 71 THR cc_start: 0.9427 (p) cc_final: 0.9052 (t) REVERT: D 272 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8766 (mmm160) REVERT: D 305 GLN cc_start: 0.6343 (mm110) cc_final: 0.6073 (mm110) REVERT: m 24 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8281 (mmm160) REVERT: m 41 ARG cc_start: 0.8317 (ttp80) cc_final: 0.8026 (ttp80) REVERT: m 47 ARG cc_start: 0.8226 (tpp-160) cc_final: 0.7444 (tpp-160) REVERT: n 61 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8848 (tp-100) REVERT: j 12 GLU cc_start: 0.8129 (tt0) cc_final: 0.7887 (tt0) REVERT: k 47 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.6992 (ttp80) REVERT: l 19 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6798 (mt-10) REVERT: d 34 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7153 (mm-30) REVERT: d 38 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: e 36 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8249 (tt) outliers start: 71 outliers final: 52 residues processed: 456 average time/residue: 0.4014 time to fit residues: 253.0402 Evaluate side-chains 459 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 402 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS 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 62 MET Chi-restraints excluded: chain C residue 110 LEU 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 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 30 LEU Chi-restraints excluded: chain c residue 48 GLN Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain a residue 53 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 21 ILE Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 291 ASN Chi-restraints excluded: chain j residue 30 LEU Chi-restraints excluded: chain j residue 34 GLU 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 43 VAL Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 16 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 36 LEU Chi-restraints excluded: chain f residue 38 GLU Chi-restraints excluded: chain f residue 63 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 chunk 59 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 154 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 133 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 217 ASN c 44 GLN g 20 GLN o 37 ASN D 275 GLN n 54 GLN e 44 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.098978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.075072 restraints weight = 59369.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.072478 restraints weight = 48746.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.072880 restraints weight = 40914.564| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19266 Z= 0.151 Angle : 0.594 11.370 25997 Z= 0.313 Chirality : 0.039 0.187 2942 Planarity : 0.004 0.058 3479 Dihedral : 4.336 33.639 2597 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.56 % Allowed : 15.66 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.17), residues: 2336 helix: 2.48 (0.13), residues: 1514 sheet: 0.50 (0.32), residues: 273 loop : 0.42 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 47 HIS 0.005 0.001 HIS B 140 PHE 0.012 0.001 PHE B 10 TYR 0.017 0.001 TYR A 95 ARG 0.009 0.001 ARG f 41 Details of bonding type rmsd hydrogen bonds : bond 0.05906 ( 1298) hydrogen bonds : angle 3.76607 ( 3831) covalent geometry : bond 0.00339 (19266) covalent geometry : angle 0.59387 (25997) *********************** 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 489 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 416 time to evaluate : 2.305 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: A 272 ARG cc_start: 0.7537 (tpp80) cc_final: 0.7099 (mpp80) REVERT: C 62 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6418 (ttt) REVERT: C 424 LYS cc_start: 0.8880 (pptt) cc_final: 0.8656 (pptt) REVERT: i 58 GLN cc_start: 0.8536 (tp40) cc_final: 0.8328 (tp40) REVERT: g 29 ASP cc_start: 0.8328 (p0) cc_final: 0.8074 (p0) REVERT: h 34 GLU cc_start: 0.6604 (tm-30) cc_final: 0.6295 (tm-30) REVERT: h 38 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6640 (mt-10) REVERT: a 24 ARG cc_start: 0.8702 (tpp80) cc_final: 0.8383 (ttm110) REVERT: a 34 GLU cc_start: 0.7544 (tp30) cc_final: 0.7190 (tp30) REVERT: b 38 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7565 (mm-30) REVERT: o 20 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7649 (tm-30) REVERT: o 52 LYS cc_start: 0.9166 (ttpp) cc_final: 0.8719 (tmmt) REVERT: p 13 LYS cc_start: 0.8899 (tmmt) cc_final: 0.8150 (tmmt) REVERT: p 17 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8027 (mp0) REVERT: p 26 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7627 (mt-10) REVERT: D 71 THR cc_start: 0.9433 (p) cc_final: 0.9047 (t) REVERT: D 272 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8802 (mmm160) REVERT: D 275 GLN cc_start: 0.8633 (mm110) cc_final: 0.8432 (mm-40) REVERT: D 305 GLN cc_start: 0.6401 (mm110) cc_final: 0.6121 (mm110) REVERT: m 24 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.8227 (mmm160) REVERT: m 41 ARG cc_start: 0.8379 (ttp80) cc_final: 0.8122 (ttp80) REVERT: m 47 ARG cc_start: 0.8207 (tpp-160) cc_final: 0.7368 (tpp-160) REVERT: n 59 ARG cc_start: 0.6959 (ttp80) cc_final: 0.6522 (tpt90) REVERT: n 61 GLN cc_start: 0.9100 (tp-100) cc_final: 0.8855 (tp-100) REVERT: k 47 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7034 (ttp80) REVERT: d 34 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7199 (mm-30) REVERT: d 38 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: e 36 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8223 (tt) REVERT: f 24 ARG cc_start: 0.7907 (mtp-110) cc_final: 0.7649 (ttm-80) outliers start: 73 outliers final: 57 residues processed: 455 average time/residue: 0.3991 time to fit residues: 250.9316 Evaluate side-chains 462 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 400 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS 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 62 MET Chi-restraints excluded: chain C residue 110 LEU 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 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 438 ILE 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 48 GLN Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain a residue 53 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 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 272 ARG Chi-restraints excluded: chain D residue 291 ASN Chi-restraints excluded: chain n residue 54 GLN Chi-restraints excluded: chain j residue 30 LEU 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 43 VAL Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 16 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 36 LEU Chi-restraints excluded: chain f residue 38 GLU Chi-restraints excluded: chain f residue 63 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 18 optimal weight: 0.7980 chunk 209 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 187 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 222 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 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 67 ASN C 41 GLN c 44 GLN g 20 GLN b 50 GLN B 67 ASN 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 = 0.3451 r_free = 0.3451 target = 0.098197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.074223 restraints weight = 58993.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.072117 restraints weight = 48410.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.072151 restraints weight = 42039.290| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4468 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= 0.167 Angle : 0.624 12.057 25997 Z= 0.327 Chirality : 0.041 0.328 2942 Planarity : 0.004 0.063 3479 Dihedral : 4.374 33.740 2595 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.71 % Allowed : 16.24 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.17), residues: 2336 helix: 2.41 (0.13), residues: 1512 sheet: 0.46 (0.32), residues: 270 loop : 0.42 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 47 HIS 0.005 0.001 HIS B 140 PHE 0.015 0.001 PHE B 10 TYR 0.017 0.002 TYR A 95 ARG 0.009 0.001 ARG D 294 Details of bonding type rmsd hydrogen bonds : bond 0.06171 ( 1298) hydrogen bonds : angle 3.83062 ( 3831) covalent geometry : bond 0.00385 (19266) covalent geometry : angle 0.62401 (25997) *********************** 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 480 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 404 time to evaluate : 2.248 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: A 272 ARG cc_start: 0.7528 (tpp80) cc_final: 0.7092 (mpp80) REVERT: C 424 LYS cc_start: 0.8919 (pptt) cc_final: 0.8709 (pptt) REVERT: i 58 GLN cc_start: 0.8583 (tp40) cc_final: 0.8346 (tp40) REVERT: g 29 ASP cc_start: 0.8342 (p0) cc_final: 0.8072 (p0) REVERT: a 24 ARG cc_start: 0.8751 (tpp80) cc_final: 0.8417 (ttm110) REVERT: a 34 GLU cc_start: 0.7589 (tp30) cc_final: 0.7227 (tp30) REVERT: o 40 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8239 (mm-30) REVERT: o 52 LYS cc_start: 0.9147 (ttpp) cc_final: 0.8711 (tmmt) REVERT: p 13 LYS cc_start: 0.8911 (tmmt) cc_final: 0.8674 (tmmt) REVERT: p 47 ARG cc_start: 0.8773 (tpp80) cc_final: 0.8573 (tpp-160) REVERT: p 63 LEU cc_start: 0.8275 (tp) cc_final: 0.8074 (tp) REVERT: D 71 THR cc_start: 0.9424 (p) cc_final: 0.9032 (t) REVERT: D 272 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8807 (mmm160) REVERT: D 275 GLN cc_start: 0.8641 (mm110) cc_final: 0.8434 (mm-40) REVERT: m 24 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8256 (mmm160) REVERT: m 41 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8133 (ttp80) REVERT: m 47 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7339 (tpp-160) REVERT: n 59 ARG cc_start: 0.7067 (ttp80) cc_final: 0.6578 (tpt90) REVERT: n 61 GLN cc_start: 0.9076 (tp-100) cc_final: 0.8836 (tp-100) REVERT: k 47 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7054 (ttp80) REVERT: e 36 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8362 (tt) outliers start: 76 outliers final: 63 residues processed: 447 average time/residue: 0.3968 time to fit residues: 245.9348 Evaluate side-chains 456 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 390 time to evaluate : 2.203 ------------------------------------------------------------------------------- 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 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 110 LEU 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 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 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 30 LEU Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 67 ASN 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 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 272 ARG Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 291 ASN Chi-restraints excluded: chain n residue 54 GLN Chi-restraints excluded: chain j residue 30 LEU 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 43 VAL Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 16 SER Chi-restraints excluded: chain l residue 45 LEU 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 36 LEU Chi-restraints excluded: chain f residue 44 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 213 optimal weight: 0.7980 chunk 204 optimal weight: 0.5980 chunk 207 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 193 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 309 GLN C 446 GLN c 44 GLN g 20 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 GLN n 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.076223 restraints weight = 59317.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.074999 restraints weight = 40802.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.075241 restraints weight = 27604.340| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4556 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= 0.157 Angle : 0.642 12.159 25997 Z= 0.335 Chirality : 0.040 0.273 2942 Planarity : 0.004 0.061 3479 Dihedral : 4.333 32.201 2595 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.51 % Allowed : 17.32 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.17), residues: 2336 helix: 2.40 (0.13), residues: 1512 sheet: 0.34 (0.32), residues: 281 loop : 0.44 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 47 HIS 0.006 0.001 HIS B 140 PHE 0.013 0.001 PHE B 10 TYR 0.017 0.002 TYR C 369 ARG 0.009 0.001 ARG p 41 Details of bonding type rmsd hydrogen bonds : bond 0.05979 ( 1298) hydrogen bonds : angle 3.80531 ( 3831) covalent geometry : bond 0.00358 (19266) covalent geometry : angle 0.64247 (25997) *********************** 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 478 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 406 time to evaluate : 2.326 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: A 47 TRP cc_start: 0.7301 (m-10) cc_final: 0.6881 (m-10) REVERT: A 272 ARG cc_start: 0.7515 (tpp80) cc_final: 0.7128 (mpp80) REVERT: i 58 GLN cc_start: 0.8576 (tp40) cc_final: 0.8320 (tp40) REVERT: g 29 ASP cc_start: 0.8336 (p0) cc_final: 0.8074 (p0) REVERT: a 24 ARG cc_start: 0.8728 (tpp80) cc_final: 0.8436 (ttm110) REVERT: a 34 GLU cc_start: 0.7517 (tp30) cc_final: 0.7169 (tp30) REVERT: a 38 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8560 (mm-30) REVERT: o 52 LYS cc_start: 0.9207 (ttpp) cc_final: 0.8761 (tmmt) REVERT: p 13 LYS cc_start: 0.8963 (tmmt) cc_final: 0.8504 (tmmt) REVERT: p 26 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7577 (mt-10) REVERT: D 71 THR cc_start: 0.9427 (p) cc_final: 0.9034 (t) REVERT: D 272 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8800 (mmm160) REVERT: D 275 GLN cc_start: 0.8806 (mm110) cc_final: 0.8596 (mm-40) REVERT: m 24 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.8296 (mmm160) REVERT: m 41 ARG cc_start: 0.8443 (ttp80) cc_final: 0.8175 (ttp80) REVERT: n 59 ARG cc_start: 0.7011 (ttp80) cc_final: 0.6476 (tpt90) REVERT: n 61 GLN cc_start: 0.9048 (tp-100) cc_final: 0.8788 (tp-100) REVERT: k 47 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7096 (ttp80) REVERT: e 36 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8302 (tt) REVERT: f 24 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7501 (ttm-80) outliers start: 72 outliers final: 61 residues processed: 450 average time/residue: 0.4074 time to fit residues: 256.0305 Evaluate side-chains 464 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 400 time to evaluate : 2.282 ------------------------------------------------------------------------------- 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 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 82 VAL Chi-restraints excluded: chain C residue 110 LEU 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 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 417 LEU 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 h residue 65 SER Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 67 ASN 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 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 272 ARG Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 291 ASN Chi-restraints excluded: chain n residue 54 GLN Chi-restraints excluded: chain j residue 30 LEU 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 43 VAL Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 16 SER Chi-restraints excluded: chain l residue 45 LEU 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 36 LEU Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain f residue 44 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 164 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 190 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 172 optimal weight: 40.0000 chunk 62 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 219 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 g 20 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.075144 restraints weight = 59204.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.073397 restraints weight = 45953.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.073126 restraints weight = 39800.134| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19266 Z= 0.165 Angle : 0.681 14.901 25997 Z= 0.352 Chirality : 0.041 0.269 2942 Planarity : 0.005 0.072 3479 Dihedral : 4.361 30.945 2595 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.41 % Allowed : 18.05 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.17), residues: 2336 helix: 2.35 (0.13), residues: 1509 sheet: 0.36 (0.32), residues: 281 loop : 0.39 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 47 HIS 0.006 0.001 HIS B 140 PHE 0.014 0.001 PHE B 10 TYR 0.020 0.002 TYR C 369 ARG 0.011 0.001 ARG D 294 Details of bonding type rmsd hydrogen bonds : bond 0.06057 ( 1298) hydrogen bonds : angle 3.85168 ( 3831) covalent geometry : bond 0.00379 (19266) covalent geometry : angle 0.68137 (25997) *********************** 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 473 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 403 time to evaluate : 2.083 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: A 272 ARG cc_start: 0.7520 (tpp80) cc_final: 0.7114 (mpp80) REVERT: i 58 GLN cc_start: 0.8627 (tp40) cc_final: 0.8374 (tp40) REVERT: g 29 ASP cc_start: 0.8334 (p0) cc_final: 0.8069 (p0) REVERT: h 34 GLU cc_start: 0.7254 (pp20) cc_final: 0.7016 (pp20) REVERT: a 24 ARG cc_start: 0.8750 (tpp80) cc_final: 0.8435 (ttm110) REVERT: a 34 GLU cc_start: 0.7566 (tp30) cc_final: 0.7278 (tp30) REVERT: o 34 GLU cc_start: 0.8183 (mp0) cc_final: 0.7913 (mp0) REVERT: o 40 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8203 (mm-30) REVERT: o 52 LYS cc_start: 0.9218 (ttpp) cc_final: 0.8785 (tmmt) REVERT: p 26 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7527 (mt-10) REVERT: D 71 THR cc_start: 0.9398 (p) cc_final: 0.8994 (t) REVERT: D 272 ARG cc_start: 0.9147 (tpt170) cc_final: 0.8818 (mmm160) REVERT: D 275 GLN cc_start: 0.8778 (mm110) cc_final: 0.8527 (mm-40) REVERT: m 41 ARG cc_start: 0.8491 (ttp80) cc_final: 0.8218 (ttp80) REVERT: n 59 ARG cc_start: 0.6979 (ttp80) cc_final: 0.6506 (tpt90) REVERT: n 61 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8780 (tp-100) REVERT: j 57 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6787 (mm-30) REVERT: k 47 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7078 (ttp80) REVERT: e 36 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8294 (tt) outliers start: 70 outliers final: 63 residues processed: 444 average time/residue: 0.4146 time to fit residues: 255.4034 Evaluate side-chains 460 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 395 time to evaluate : 2.346 ------------------------------------------------------------------------------- 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 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 40 THR Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 110 LEU 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 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 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 c residue 30 LEU Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 67 ASN 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 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 291 ASN Chi-restraints excluded: chain n residue 54 GLN Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain j residue 30 LEU 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 43 VAL Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain l residue 16 SER Chi-restraints excluded: chain l residue 45 LEU 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 e residue 64 LEU Chi-restraints excluded: chain f residue 44 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 70 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 76 optimal weight: 0.0970 chunk 66 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.075381 restraints weight = 59293.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.074358 restraints weight = 40093.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.074652 restraints weight = 27862.429| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19266 Z= 0.167 Angle : 0.702 13.441 25997 Z= 0.363 Chirality : 0.041 0.246 2942 Planarity : 0.005 0.082 3479 Dihedral : 4.318 24.363 2593 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.27 % Allowed : 18.44 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.17), residues: 2336 helix: 2.32 (0.13), residues: 1513 sheet: 0.40 (0.32), residues: 281 loop : 0.34 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 47 HIS 0.006 0.001 HIS B 140 PHE 0.014 0.001 PHE A 39 TYR 0.022 0.002 TYR C 369 ARG 0.010 0.001 ARG D 294 Details of bonding type rmsd hydrogen bonds : bond 0.06056 ( 1298) hydrogen bonds : angle 3.85243 ( 3831) covalent geometry : bond 0.00387 (19266) covalent geometry : angle 0.70192 (25997) ********************** 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 466 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 399 time to evaluate : 2.373 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: A 272 ARG cc_start: 0.7494 (tpp80) cc_final: 0.7121 (mpp80) REVERT: C 419 LYS cc_start: 0.8527 (tppt) cc_final: 0.8092 (mmmm) REVERT: i 58 GLN cc_start: 0.8581 (tp40) cc_final: 0.8312 (tp40) REVERT: g 29 ASP cc_start: 0.8324 (p0) cc_final: 0.8071 (p0) REVERT: a 24 ARG cc_start: 0.8760 (tpp80) cc_final: 0.8474 (ttm110) REVERT: a 34 GLU cc_start: 0.7599 (tp30) cc_final: 0.7177 (tp30) REVERT: o 34 GLU cc_start: 0.8194 (mp0) cc_final: 0.7919 (mp0) REVERT: o 52 LYS cc_start: 0.9218 (ttpp) cc_final: 0.8767 (tmmt) REVERT: p 26 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7552 (mt-10) REVERT: D 71 THR cc_start: 0.9424 (p) cc_final: 0.9016 (t) REVERT: D 272 ARG cc_start: 0.9096 (tpt170) cc_final: 0.8806 (mmm160) REVERT: D 305 GLN cc_start: 0.6132 (mm-40) cc_final: 0.5864 (mm-40) REVERT: m 24 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8107 (mmm160) REVERT: m 41 ARG cc_start: 0.8307 (ttp80) cc_final: 0.8050 (ttp80) REVERT: n 61 GLN cc_start: 0.9066 (tp-100) cc_final: 0.8751 (tp-100) REVERT: j 12 GLU cc_start: 0.8167 (tt0) cc_final: 0.7883 (tt0) REVERT: j 57 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6829 (mm-30) REVERT: k 47 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7080 (ttp80) REVERT: l 63 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8586 (mt) REVERT: e 36 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8332 (tt) outliers start: 67 outliers final: 63 residues processed: 438 average time/residue: 0.4308 time to fit residues: 264.1539 Evaluate side-chains 461 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 395 time to evaluate : 2.172 ------------------------------------------------------------------------------- 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 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 40 THR Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 110 LEU 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 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 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 c residue 30 LEU Chi-restraints excluded: chain h residue 65 SER Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 67 ASN 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 44 GLN 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 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 291 ASN Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain j residue 30 LEU 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 43 VAL Chi-restraints excluded: chain k residue 47 ARG Chi-restraints excluded: chain k residue 65 SER Chi-restraints excluded: chain l residue 16 SER Chi-restraints excluded: chain l residue 45 LEU Chi-restraints excluded: chain l residue 63 LEU 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 e residue 64 LEU Chi-restraints excluded: chain f residue 44 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 49 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 179 optimal weight: 40.0000 chunk 88 optimal weight: 0.7980 chunk 119 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN C 41 GLN c 44 GLN c 54 GLN g 20 GLN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN ** n 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.074966 restraints weight = 59081.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074006 restraints weight = 41199.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.074397 restraints weight = 29392.307| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4705 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= 0.169 Angle : 0.714 12.859 25997 Z= 0.369 Chirality : 0.041 0.234 2942 Planarity : 0.005 0.082 3479 Dihedral : 4.354 24.445 2593 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.51 % Allowed : 18.63 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.17), residues: 2336 helix: 2.31 (0.13), residues: 1512 sheet: 0.40 (0.32), residues: 281 loop : 0.29 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 47 HIS 0.004 0.001 HIS B 140 PHE 0.016 0.001 PHE A 39 TYR 0.021 0.002 TYR C 369 ARG 0.012 0.001 ARG D 294 Details of bonding type rmsd hydrogen bonds : bond 0.06077 ( 1298) hydrogen bonds : angle 3.87550 ( 3831) covalent geometry : bond 0.00392 (19266) covalent geometry : angle 0.71391 (25997) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8519.00 seconds wall clock time: 148 minutes 46.16 seconds (8926.16 seconds total)